Core
momapy.celldesigner.core
Classes:
| Name | Description |
|---|---|
AndGate |
Class for and gates |
AndGateLayout |
Class for and gate layouts |
AntisenseRNA |
Class for antisense RNAs |
AntisenseRNALayout |
Class for antisense RNA layouts |
AntisenseRNATemplate |
Class for antisense RNA templates |
BooleanLogicGate |
Base class for Boolean logic gates |
Catalysis |
Class for catalyses |
CatalysisLayout |
Class for catalysis layouts |
Catalyzer |
Class for catalyzers |
CellDesignerDoubleHeadedArc |
Base class for CellDesigner double-headed arcs |
CellDesignerLayout |
Class for CellDesigner layouts |
CellDesignerMap |
Class for CellDesigner maps |
CellDesignerModel |
Class for CellDesigner models |
CellDesignerModelElement |
Base class for CellDesigner model elements |
CellDesignerNode |
Base class for CellDesigner nodes |
CellDesignerSingleHeadedArc |
Base class for CellDesigner single-headed arcs |
CodingRegion |
Class for coding regions |
Compartment |
Class for compartments |
Complex |
Class for complexes |
ComplexLayout |
Class for complex layouts |
ConsumptionLayout |
Class for consumption layouts |
Degraded |
Class for degradeds |
DegradedLayout |
Class for degraded layouts |
Dissociation |
Class for dissociations |
DissociationLayout |
Class for dissociation layouts |
Drug |
Class for drugs |
DrugLayout |
Class for drug layouts |
Gene |
Class for genes |
GeneLayout |
Class for gene layouts |
GeneTemplate |
Class for gene templates |
GenericProtein |
Class for generic proteins |
GenericProteinLayout |
Class for generic protein layouts |
GenericProteinTemplate |
Class for generic protein templates |
HeterodimerAssociation |
Class for heterodimer associations |
HeterodimerAssociationLayout |
Class for heterodimer association layouts |
Inhibition |
Class for inhibitions |
InhibitionLayout |
Class for inhibition layouts |
Inhibitor |
Class for inhibitors |
Ion |
Class for ions |
IonChannel |
Class for ion channels |
IonChannelLayout |
Class for generic ion channel layouts |
IonChannelTemplate |
Class for ion channel templates |
IonLayout |
Class for ion layouts |
KnownTransitionOmitted |
Class for known transitions omitted |
KnownTransitionOmittedLayout |
Class for known transition omitted layouts |
LogicArcLayout |
Class for logic arc layouts |
Modification |
Class for modifications |
ModificationLayout |
Class for modification layouts |
ModificationResidue |
Class for modification residues |
ModificationSite |
Class for modification sites |
ModificationState |
Class for modification states |
Modulation |
Class for modulations |
ModulationLayout |
Class for modulation layouts |
Modulator |
Class for modulators |
NegativeInfluence |
Class for negative influences |
NotGate |
Class for not gates |
NotGateLayout |
Class for not gate layouts |
OrGate |
Class for or gates |
OrGateLayout |
Class for or gate layouts |
OvalCompartmentLayout |
Class for oval compartment layouts |
Phenotype |
Class for phenotypes |
PhenotypeLayout |
Class for phenotype layouts |
PhysicalStimulation |
Class for physical stimulations |
PhysicalStimulationLayout |
Class for physical stimulation layouts |
PhysicalStimulator |
Class for physical stimulators |
PositiveInfluence |
Class for positive influences |
PositiveInfluenceLayout |
Class for positive influence layouts |
Product |
Class for products |
ProductionLayout |
Class for production layouts |
Protein |
Base class for proteins |
ProteinBindingDomain |
Class for protein binding domains |
ProteinTemplate |
Base class for protein templates |
RNA |
Class for RNAs |
RNALayout |
Class for RNA layouts |
RNATemplate |
Class for RNA templates |
Reactant |
Class for reactants |
Reaction |
Base class for reactions |
Receptor |
Class for receptors |
ReceptorLayout |
Class for receptor layouts |
ReceptorTemplate |
Class for receptor templates |
RectangleCompartmentLayout |
Class for rectangle compartment layouts |
Region |
Class for regions |
RegulatoryRegion |
Class for regulatory regions |
SimpleMolecule |
Class for simple molecules |
SimpleMoleculeLayout |
Class for simple chemical layouts |
Species |
Base class for species |
SpeciesTemplate |
Base class for species templates |
StateTransition |
Class for state transitions |
StateTransitionLayout |
Class for state transition layouts |
StructuralState |
Class for structural states |
StructuralStateLayout |
Class for structural states layouts |
Transcription |
Class for transcriptions |
TranscriptionLayout |
Class for transcription layouts |
TranscriptionStartingSiteL |
Class for left transcription starting sites |
TranscriptionStartingSiteR |
Class for right transcription starting sites |
Translation |
Class for translation |
TranslationLayout |
Class for translation layouts |
Transport |
Class for transports |
TransportLayout |
Class for transport layouts |
Trigger |
Class for triggers |
Triggering |
Class for triggerings |
TriggeringLayout |
Class for triggering layouts |
TruncatedProtein |
Class for truncated proteins |
TruncatedProteinLayout |
Class for truncated protein layouts |
TruncatedProteinTemplate |
Class for truncated protein templates |
Truncation |
Class for truncations |
TruncationLayout |
Class for truncation layouts |
Unknown |
Class for unknown species |
UnknownCatalysis |
Class for unknown catalyses |
UnknownCatalysisLayout |
Class for unknown catalysis layouts |
UnknownCatalyzer |
Class for unknown catalyzers |
UnknownGate |
Class for unknown gates |
UnknownGateLayout |
Class for unknown gate layouts |
UnknownInhibition |
Class for unknown inhibitions |
UnknownInhibitionLayout |
Class for unknown inhibition layouts |
UnknownInhibitor |
Class for unknown inhibitors |
UnknownLayout |
Class for unknown species layouts |
UnknownModulation |
Class for unknown modulations |
UnknownModulationLayout |
Class for unknown modulation layouts |
UnknownModulator |
Class for unknown modulators |
UnknownNegativeInfluence |
Class for unknown negative influences |
UnknownPhysicalStimulation |
Class for unknown physical stimulations |
UnknownPhysicalStimulationLayout |
Class for unknown physical stimulation layouts |
UnknownPositiveInfluence |
Class for unknown positive influences |
UnknownPositiveInfluenceLayout |
Class for unknown positive influence layouts |
UnknownTransition |
Class for unknown transitions |
UnknownTransitionLayout |
Class for unknown transition layouts |
UnknownTriggering |
Class for unknown triggerings |
UnknownTriggeringLayout |
Class for unknown triggering layouts |
AndGate
dataclass
AndGate(
*,
id_: str = get_uuid4_as_str(),
inputs: frozenset[Species] = frozenset()
)
Bases: BooleanLogicGate
Class for and gates
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'5b675587-4858-4739-9852-df1e671e8ee4'
|
AndGateLayout
dataclass
AndGateLayout(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float = 15.0,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 15.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None
)
Bases: _SimpleNodeMixin, _TextMixin, CellDesignerNode
Class for and gate layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'831bb35b-671e-4713-9bee-6c008d38e2fd'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
15.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
15.0
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
label_center |
Return the label center anchor of the node |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
830 831 832 833 834 835 836 837 838 839 840 841 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/core.py
719 720 721 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
711 712 713 714 715 716 717 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
723 724 725 726 727 728 729 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
label_center
label_center() -> Point
Return the label center anchor of the node
Source code in src/momapy/core.py
791 792 793 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/core.py
691 692 693 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
703 704 705 706 707 708 709 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
695 696 697 698 699 700 701 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
683 684 685 686 687 688 689 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
675 676 677 678 679 680 681 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/core.py
747 748 749 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
731 732 733 734 735 736 737 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
739 740 741 742 743 744 745 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
751 752 753 754 755 756 757 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
759 760 761 762 763 764 765 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/core.py
775 776 777 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
779 780 781 782 783 784 785 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
767 768 769 770 771 772 773 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
AntisenseRNA
dataclass
AntisenseRNA(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
compartment: Compartment | None = None,
hypothetical: bool = False,
active: bool = False,
homomultimer: int = 1,
template: AntisenseRNATemplate,
modifications: frozenset[Modification] = frozenset()
)
Bases: Species
Class for antisense RNAs
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'236fb9b0-ba8b-4591-8b63-a8a281cb784f'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
compartment
|
Compartment | None
|
|
None
|
hypothetical
|
bool
|
Whether the species is hypothetical or not |
False
|
active
|
bool
|
Whether the species is active or not |
False
|
homomultimer
|
int
|
The number of subunits forming the species |
1
|
template
|
AntisenseRNATemplate
|
|
required |
AntisenseRNALayout
dataclass
AntisenseRNALayout(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
offset: float = 3.0,
subunits_stroke: (
tuple[NoneValueType | Color] | None
) = None,
subunits_stroke_width: (
tuple[NoneValueType | float] | None
) = None,
subunits_stroke_dasharray: (
tuple[NoneValueType | tuple[float]] | None
) = None,
subunits_stroke_dashoffset: tuple[float] | None = None,
subunits_fill: (
tuple[NoneValueType | Color] | None
) = None,
subunits_transform: (
tuple[NoneValueType | tuple[Transformation]] | None
) = None,
subunits_filter: (
tuple[NoneValueType | Filter] | None
) = None,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float = 30.0,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 60.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
n: int = 1,
angle: float = 45.0
)
Bases: _MultiNodeMixin, CellDesignerNode
Class for antisense RNA layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'b7c4ac2e-cc74-4fda-8c97-e1a9567a43f1'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
30.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
60.0
|
offset
|
float
|
|
3.0
|
subunits_stroke
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_stroke_width
|
tuple[Union[NoneValueType, float]] | None
|
|
None
|
subunits_stroke_dasharray
|
tuple[Union[NoneValueType, tuple[float]]] | None
|
|
None
|
subunits_stroke_dashoffset
|
tuple[float] | None
|
|
None
|
subunits_fill
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_transform
|
tuple[Union[NoneValueType, tuple[Transformation]]] | None
|
|
None
|
subunits_filter
|
tuple[Union[NoneValueType, Filter]] | None
|
|
None
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
n
|
int
|
|
1
|
angle
|
float
|
|
45.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
angle |
float
|
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
class-attribute
instance-attribute
angle: float = 45.0
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/celldesigner/core.py
1634 1635 1636 1637 1638 1639 1640 1641 1642 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/celldesigner/core.py
1624 1625 1626 1627 1628 1629 1630 1631 1632 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/celldesigner/core.py
1644 1645 1646 1647 1648 1649 1650 1651 1652 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/celldesigner/core.py
1594 1595 1596 1597 1598 1599 1600 1601 1602 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/celldesigner/core.py
1614 1615 1616 1617 1618 1619 1620 1621 1622 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/celldesigner/core.py
1604 1605 1606 1607 1608 1609 1610 1611 1612 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/celldesigner/core.py
1584 1585 1586 1587 1588 1589 1590 1591 1592 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/celldesigner/core.py
1574 1575 1576 1577 1578 1579 1580 1581 1582 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/celldesigner/core.py
1674 1675 1676 1677 1678 1679 1680 1681 1682 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/celldesigner/core.py
1654 1655 1656 1657 1658 1659 1660 1661 1662 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/celldesigner/core.py
1664 1665 1666 1667 1668 1669 1670 1671 1672 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/celldesigner/core.py
1684 1685 1686 1687 1688 1689 1690 1691 1692 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/celldesigner/core.py
1694 1695 1696 1697 1698 1699 1700 1701 1702 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/celldesigner/core.py
1714 1715 1716 1717 1718 1719 1720 1721 1722 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/celldesigner/core.py
1724 1725 1726 1727 1728 1729 1730 1731 1732 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/celldesigner/core.py
1704 1705 1706 1707 1708 1709 1710 1711 1712 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
AntisenseRNATemplate
dataclass
AntisenseRNATemplate(
*,
id_: str = get_uuid4_as_str(),
name: str,
regions: frozenset[
ModificationSite
| CodingRegion
| ProteinBindingDomain
] = frozenset()
)
Bases: SpeciesTemplate
Class for antisense RNA templates
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'34c0ed06-e253-4514-8a2d-e25c8a57eba5'
|
name
|
str
|
The name of the species template |
required |
BooleanLogicGate
dataclass
BooleanLogicGate(
*,
id_: str = get_uuid4_as_str(),
inputs: frozenset[Species] = frozenset()
)
Bases: CellDesignerModelElement
Base class for Boolean logic gates
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'46b4bf60-e5c1-4636-bb6b-a88e46dbe8b4'
|
Catalysis
dataclass
Catalysis(
*,
id_: str = get_uuid4_as_str(),
source: Species | BooleanLogicGate,
target: Species | None
)
Bases: Modulation
Class for catalyses
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'f9b16ce1-6b1f-44a1-aea4-5db031b2aea3'
|
source
|
Species | BooleanLogicGate
|
The source of the influence |
required |
target
|
Species | None
|
The target of the influence |
required |
CatalysisLayout
dataclass
CatalysisLayout(
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 0.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 0.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_fill: NoneValueType | Color | None = white,
arrowhead_filter: NoneValueType | Filter | None = None,
arrowhead_stroke: NoneValueType | Color | None = black,
arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
arrowhead_stroke_dashoffset: float | None = None,
arrowhead_stroke_width: float | None = 1.0,
arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_height: float = 7.0,
arrowhead_width: float = 7.0
)
Bases: CellDesignerSingleHeadedArc
Class for catalysis layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'fcbca2ac-6cd8-4fb3-90c0-d653366242d7'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
The length the end of the arc will be shorten by |
0.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The path stroke dasharray of the arc |
None
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
The length the start of the arc will be shorten by |
0.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
arrowhead_filter
|
NoneValueType | Filter | None
|
The arrowhead filter of the arc |
None
|
arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The arrowhead stroke dasharray of the arc |
None
|
arrowhead_stroke_dashoffset
|
float | None
|
The arrowhead stroke dashoffset of the arc |
None
|
arrowhead_stroke_width
|
float | None
|
|
1.0
|
arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
The arrowhead transform of the arc |
None
|
arrowhead_height
|
float
|
|
7.0
|
arrowhead_width
|
float
|
|
7.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
1089 1090 1091 1092 1093 1094 1095 1096 1097 | |
arrowhead_bbox
arrowhead_bbox() -> Bbox
Return the bounding box of the single-headed arc arrowhead
Source code in src/momapy/core.py
1099 1100 1101 1102 1103 | |
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 | |
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 | |
arrowhead_length
arrowhead_length() -> float
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
1071 1072 1073 1074 1075 1076 1077 1078 | |
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
1080 1081 1082 1083 1084 1085 1086 1087 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
Catalyzer
dataclass
Catalyzer(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
referred_species: Species | BooleanLogicGate
)
Bases: PhysicalStimulator
Class for catalyzers
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'5edd041c-8ba7-46f8-a284-49447f771834'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
referred_species
|
Species | BooleanLogicGate
|
The species the modifier refers to |
required |
CellDesignerDoubleHeadedArc
dataclass
CellDesignerDoubleHeadedArc(
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 0.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 0.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_arrowhead_fill: NoneValueType | Color | None = None,
end_arrowhead_filter: (
NoneValueType | Filter | None
) = None,
end_arrowhead_stroke: (
NoneValueType | Color | None
) = None,
end_arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
end_arrowhead_stroke_dashoffset: float | None = None,
end_arrowhead_stroke_width: float | None = None,
end_arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
start_arrowhead_fill: (
NoneValueType | Color | None
) = None,
start_arrowhead_filter: (
NoneValueType | Filter | None
) = None,
start_arrowhead_stroke: (
NoneValueType | Color | None
) = None,
start_arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
start_arrowhead_stroke_dashoffset: float | None = None,
start_arrowhead_stroke_width: float | None = None,
start_arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None
)
Bases: DoubleHeadedArc
Base class for CellDesigner double-headed arcs
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'fa319af6-07f8-431b-9ca4-d3a9efcc741b'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
The length the end of the arc will be shorten by |
0.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The path stroke dasharray of the arc |
None
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
The length the start of the arc will be shorten by |
0.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
end_arrowhead_fill
|
NoneValueType | Color | None
|
The end arrowhead fill color of the arc |
None
|
end_arrowhead_filter
|
NoneValueType | Filter | None
|
The end arrowhead filter of the arc |
None
|
end_arrowhead_stroke
|
NoneValueType | Color | None
|
The end arrowhead stroke color of the arc |
None
|
end_arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The end arrowhead stroke dasharray of the arc |
None
|
end_arrowhead_stroke_dashoffset
|
float | None
|
The end arrowhead stroke dashoffset of the arc |
None
|
end_arrowhead_stroke_width
|
float | None
|
The end arrowhead stroke width of the arc |
None
|
end_arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
The end arrowhead transform of the arc |
None
|
start_arrowhead_fill
|
NoneValueType | Color | None
|
The start arrowhead fill color of the arc |
None
|
start_arrowhead_filter
|
NoneValueType | Filter | None
|
The start arrowhead filter of the arc |
None
|
start_arrowhead_stroke
|
NoneValueType | Color | None
|
The start arrowhead stroke color of the arc |
None
|
start_arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The start arrowhead stroke dasharray of the arc |
None
|
start_arrowhead_stroke_dashoffset
|
float | None
|
The start arrowhead stroke dashoffset of the arc |
None
|
start_arrowhead_stroke_width
|
float | None
|
The start arrowhead stroke width of the arc |
None
|
start_arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
The start arrowhead transform of the arc |
None
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_arrowhead_base |
Return the base anchor point of the double-headed arc end arrowhead |
end_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
end_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. |
end_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc end arrowhead |
end_arrowhead_length |
Return the length of the double-headed arc end arrowhead |
end_arrowhead_tip |
Return the tip anchor point of the double-headed arc end arrowhead |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the double-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_arrowhead_base |
Return the base anchor point of the double-headed arc start arrowhead |
start_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
start_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. |
start_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc start arrowhead |
start_arrowhead_length |
Return the length of the double-headed arc start arrowhead |
start_arrowhead_tip |
Return the tip anchor point of the double-headed arc start arrowhead |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_arrowhead_base
end_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 | |
end_arrowhead_bbox
end_arrowhead_bbox()
Return the bounding box of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1400 1401 1402 1403 1404 | |
end_arrowhead_border
end_arrowhead_border(point)
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 | |
end_arrowhead_drawing_elements
end_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 | |
end_arrowhead_length
end_arrowhead_length() -> float
Return the length of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1370 1371 1372 1373 1374 1375 1376 1377 | |
end_arrowhead_tip
end_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1379 1380 1381 1382 1383 1384 1385 1386 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the double-headed arc path
Source code in src/momapy/core.py
1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
Source code in src/momapy/celldesigner/core.py
793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_arrowhead_base
start_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 | |
start_arrowhead_bbox
start_arrowhead_bbox() -> Bbox
Return the bounding box of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1353 1354 1355 1356 1357 | |
start_arrowhead_border
start_arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 | |
start_arrowhead_drawing_elements
start_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 | |
start_arrowhead_length
start_arrowhead_length() -> float
Return the length of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1321 1322 1323 1324 1325 1326 1327 1328 | |
start_arrowhead_tip
start_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1330 1331 1332 1333 1334 1335 1336 1337 1338 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
CellDesignerLayout
dataclass
CellDesignerLayout(
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
fill: NoneValueType | Color | None = NoneValue,
filter: NoneValueType | Filter | None = None,
height: float,
label: TextLayout | None = None,
position: Point,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = None
)
Bases: Layout
Class for CellDesigner layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'46dfebe5-1c6d-444a-bba7-490ed3bd17c4'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
The height of the node |
required |
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
The stroke color of the node |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
The stroke width of the node |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
The stroke width of the node |
None
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
is_sublayout |
Return |
label_center |
Return the label center anchor of the node |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
830 831 832 833 834 835 836 837 838 839 840 841 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/core.py
719 720 721 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
711 712 713 714 715 716 717 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
723 724 725 726 727 728 729 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
is_sublayout
is_sublayout(other, flattened=False, unordered=False)
Return true if another given layout is a sublayout of the layout, false otherwise
Source code in src/momapy/core.py
1615 1616 1617 1618 1619 1620 1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 1635 1636 1637 1638 1639 1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650 1651 | |
label_center
label_center() -> Point
Return the label center anchor of the node
Source code in src/momapy/core.py
791 792 793 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/core.py
691 692 693 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
703 704 705 706 707 708 709 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
695 696 697 698 699 700 701 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
683 684 685 686 687 688 689 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
675 676 677 678 679 680 681 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/core.py
747 748 749 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
731 732 733 734 735 736 737 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
739 740 741 742 743 744 745 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
751 752 753 754 755 756 757 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
759 760 761 762 763 764 765 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/core.py
775 776 777 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
779 780 781 782 783 784 785 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
767 768 769 770 771 772 773 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
CellDesignerMap
dataclass
CellDesignerMap(
*,
id_: str = get_uuid4_as_str(),
model: CellDesignerModel | None = None,
layout: CellDesignerLayout | None = None,
layout_model_mapping: LayoutModelMapping | None = None
)
Bases: Map
Class for CellDesigner maps
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'0f30fb73-18e9-4444-8a12-c1b4aefcc67a'
|
model
|
CellDesignerModel | None
|
|
None
|
layout
|
CellDesignerLayout | None
|
|
None
|
layout_model_mapping
|
LayoutModelMapping | None
|
The layout model mapping of the map |
None
|
Methods:
| Name | Description |
|---|---|
get_mapping |
Return the layout elements mapped to the given model element |
is_submap |
Return |
get_mapping
get_mapping(
key: (
ModelElement | _MappingElementType | _MappingKeyType
),
expand: bool = True,
unpack: bool = False,
)
Return the layout elements mapped to the given model element
Source code in src/momapy/core.py
1778 1779 1780 1781 1782 1783 1784 1785 1786 1787 | |
is_submap
is_submap(other)
Return true if another given map is a submap of the Map, false otherwise
Source code in src/momapy/core.py
1768 1769 1770 1771 1772 1773 1774 1775 1776 | |
CellDesignerModel
dataclass
CellDesignerModel(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
compartments: frozenset[Compartment] = frozenset(),
species: frozenset[Species] = frozenset(),
reactions: frozenset[Reaction] = frozenset(),
species_templates: frozenset[
SpeciesTemplate
] = frozenset(),
boolean_logic_gates: frozenset[
BooleanLogicGate
] = frozenset(),
modulations: frozenset[
Modulation | UnknownModulation
] = frozenset()
)
Bases: Model
Class for CellDesigner models
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'6b2ffa2e-9f42-4ed9-a5bf-f1da13d0baac'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
CellDesignerModelElement
dataclass
CellDesignerModelElement(*, id_: str = get_uuid4_as_str())
Bases: ModelElement
Base class for CellDesigner model elements
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'9e487fdc-a3a0-485f-bdc7-c92ea386dcb3'
|
CellDesignerNode
dataclass
CellDesignerNode(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = None
)
Bases: SBGNNode
Base class for CellDesigner nodes
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'358fe1e3-b67a-48f6-8dbc-ffca538ce8fd'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
The height of the node |
required |
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
The stroke width of the node |
None
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
label_center |
Return the label center anchor of the node |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
830 831 832 833 834 835 836 837 838 839 840 841 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/core.py
719 720 721 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
711 712 713 714 715 716 717 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
723 724 725 726 727 728 729 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
label_center
label_center() -> Point
Return the label center anchor of the node
Source code in src/momapy/core.py
791 792 793 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/core.py
691 692 693 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
703 704 705 706 707 708 709 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
695 696 697 698 699 700 701 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
683 684 685 686 687 688 689 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
675 676 677 678 679 680 681 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/core.py
747 748 749 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
731 732 733 734 735 736 737 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
739 740 741 742 743 744 745 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
751 752 753 754 755 756 757 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
759 760 761 762 763 764 765 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/core.py
775 776 777 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
779 780 781 782 783 784 785 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
767 768 769 770 771 772 773 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
CellDesignerSingleHeadedArc
dataclass
CellDesignerSingleHeadedArc(
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 0.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 0.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_fill: NoneValueType | Color | None = None,
arrowhead_filter: NoneValueType | Filter | None = None,
arrowhead_stroke: NoneValueType | Color | None = black,
arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
arrowhead_stroke_dashoffset: float | None = None,
arrowhead_stroke_width: float | None = 1.0,
arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None
)
Bases: SingleHeadedArc
Base class for CellDesigner single-headed arcs
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'b226c007-f59b-4211-8f2a-838c41566e36'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
The length the end of the arc will be shorten by |
0.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The path stroke dasharray of the arc |
None
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
The length the start of the arc will be shorten by |
0.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
arrowhead_fill
|
NoneValueType | Color | None
|
The arrowhead fill color of the arc |
None
|
arrowhead_filter
|
NoneValueType | Filter | None
|
The arrowhead filter of the arc |
None
|
arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The arrowhead stroke dasharray of the arc |
None
|
arrowhead_stroke_dashoffset
|
float | None
|
The arrowhead stroke dashoffset of the arc |
None
|
arrowhead_stroke_width
|
float | None
|
|
1.0
|
arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
The arrowhead transform of the arc |
None
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
1089 1090 1091 1092 1093 1094 1095 1096 1097 | |
arrowhead_bbox
arrowhead_bbox() -> Bbox
Return the bounding box of the single-headed arc arrowhead
Source code in src/momapy/core.py
1099 1100 1101 1102 1103 | |
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 | |
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 | |
arrowhead_length
arrowhead_length() -> float
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
1071 1072 1073 1074 1075 1076 1077 1078 | |
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
1080 1081 1082 1083 1084 1085 1086 1087 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
CodingRegion
dataclass
CodingRegion(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
active: bool = False
)
Bases: Region
Class for coding regions
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'cdbb70e5-c9a0-477d-9229-dd265229e473'
|
name
|
str | None
|
The name of the region |
None
|
active
|
bool
|
Whether the region is active or not |
False
|
Compartment
dataclass
Compartment(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
outside: Optional[
ForwardRef(Compartment, module=core)
] = None
)
Bases: Compartment, CellDesignerModelElement
Class for compartments
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'81da502d-1f41-4c55-a707-698962e0c283'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
outside
|
ForwardRef(Compartment, module=core) | None
|
|
None
|
Complex
dataclass
Complex(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
compartment: Compartment | None = None,
hypothetical: bool = False,
active: bool = False,
homomultimer: int = 1,
structural_states: frozenset[
StructuralState
] = frozenset(),
subunits: frozenset[Species] = frozenset()
)
Bases: Species
Class for complexes
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'4910a194-9dca-474b-a0e0-d2eb1f7bcb4e'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
compartment
|
Compartment | None
|
|
None
|
hypothetical
|
bool
|
Whether the species is hypothetical or not |
False
|
active
|
bool
|
Whether the species is active or not |
False
|
homomultimer
|
int
|
The number of subunits forming the species |
1
|
ComplexLayout
dataclass
ComplexLayout(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
offset: float = 3.0,
subunits_stroke: (
tuple[NoneValueType | Color] | None
) = None,
subunits_stroke_width: (
tuple[NoneValueType | float] | None
) = None,
subunits_stroke_dasharray: (
tuple[NoneValueType | tuple[float]] | None
) = None,
subunits_stroke_dashoffset: tuple[float] | None = None,
subunits_fill: (
tuple[NoneValueType | Color] | None
) = None,
subunits_transform: (
tuple[NoneValueType | tuple[Transformation]] | None
) = None,
subunits_filter: (
tuple[NoneValueType | Filter] | None
) = None,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float = 30.0,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 60.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
n: int = 1,
cut_corners: float = 6.0
)
Bases: _MultiNodeMixin, CellDesignerNode
Class for complex layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'0b7b5e3b-949a-4c67-bbff-3971feaecd9b'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
30.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
60.0
|
offset
|
float
|
|
3.0
|
subunits_stroke
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_stroke_width
|
tuple[Union[NoneValueType, float]] | None
|
|
None
|
subunits_stroke_dasharray
|
tuple[Union[NoneValueType, tuple[float]]] | None
|
|
None
|
subunits_stroke_dashoffset
|
tuple[float] | None
|
|
None
|
subunits_fill
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_transform
|
tuple[Union[NoneValueType, tuple[Transformation]]] | None
|
|
None
|
subunits_filter
|
tuple[Union[NoneValueType, Filter]] | None
|
|
None
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
n
|
int
|
|
1
|
cut_corners
|
float
|
|
6.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
830 831 832 833 834 835 836 837 838 839 840 841 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/core.py
719 720 721 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
711 712 713 714 715 716 717 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
723 724 725 726 727 728 729 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/core.py
691 692 693 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
703 704 705 706 707 708 709 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
695 696 697 698 699 700 701 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
683 684 685 686 687 688 689 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
675 676 677 678 679 680 681 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/core.py
747 748 749 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
731 732 733 734 735 736 737 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
739 740 741 742 743 744 745 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
751 752 753 754 755 756 757 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
759 760 761 762 763 764 765 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/core.py
775 776 777 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
779 780 781 782 783 784 785 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
767 768 769 770 771 772 773 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
ConsumptionLayout
dataclass
ConsumptionLayout(
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 0.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 0.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_fill: NoneValueType | Color | None = None,
arrowhead_filter: NoneValueType | Filter | None = None,
arrowhead_stroke: NoneValueType | Color | None = black,
arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
arrowhead_stroke_dashoffset: float | None = None,
arrowhead_stroke_width: float | None = 1.0,
arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None
)
Bases: CellDesignerSingleHeadedArc
Class for consumption layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'b53cf356-b30c-47c5-9625-ece9eeac2e08'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
The length the end of the arc will be shorten by |
0.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The path stroke dasharray of the arc |
None
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
The length the start of the arc will be shorten by |
0.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
arrowhead_fill
|
NoneValueType | Color | None
|
The arrowhead fill color of the arc |
None
|
arrowhead_filter
|
NoneValueType | Filter | None
|
The arrowhead filter of the arc |
None
|
arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The arrowhead stroke dasharray of the arc |
None
|
arrowhead_stroke_dashoffset
|
float | None
|
The arrowhead stroke dashoffset of the arc |
None
|
arrowhead_stroke_width
|
float | None
|
|
1.0
|
arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
The arrowhead transform of the arc |
None
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
1089 1090 1091 1092 1093 1094 1095 1096 1097 | |
arrowhead_bbox
arrowhead_bbox() -> Bbox
Return the bounding box of the single-headed arc arrowhead
Source code in src/momapy/core.py
1099 1100 1101 1102 1103 | |
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 | |
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 | |
arrowhead_length
arrowhead_length() -> float
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
1071 1072 1073 1074 1075 1076 1077 1078 | |
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
1080 1081 1082 1083 1084 1085 1086 1087 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
Degraded
dataclass
Degraded(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
compartment: Compartment | None = None,
hypothetical: bool = False,
active: bool = False,
homomultimer: int = 1
)
Bases: Species
Class for degradeds
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'b254bd90-0b4a-4b7a-8c0c-1f806b16ff41'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
compartment
|
Compartment | None
|
|
None
|
hypothetical
|
bool
|
Whether the species is hypothetical or not |
False
|
active
|
bool
|
Whether the species is active or not |
False
|
homomultimer
|
int
|
The number of subunits forming the species |
1
|
DegradedLayout
dataclass
DegradedLayout(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
offset: float = 3.0,
subunits_stroke: (
tuple[NoneValueType | Color] | None
) = None,
subunits_stroke_width: (
tuple[NoneValueType | float] | None
) = None,
subunits_stroke_dasharray: (
tuple[NoneValueType | tuple[float]] | None
) = None,
subunits_stroke_dashoffset: tuple[float] | None = None,
subunits_fill: (
tuple[NoneValueType | Color] | None
) = None,
subunits_transform: (
tuple[NoneValueType | tuple[Transformation]] | None
) = None,
subunits_filter: (
tuple[NoneValueType | Filter] | None
) = None,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float = 30.0,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 30.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
n: int = 1
)
Bases: _MultiNodeMixin, CellDesignerNode
Class for degraded layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'10c8489e-f2e0-4a6a-a864-97c3cc01d4f5'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
30.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
30.0
|
offset
|
float
|
|
3.0
|
subunits_stroke
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_stroke_width
|
tuple[Union[NoneValueType, float]] | None
|
|
None
|
subunits_stroke_dasharray
|
tuple[Union[NoneValueType, tuple[float]]] | None
|
|
None
|
subunits_stroke_dashoffset
|
tuple[float] | None
|
|
None
|
subunits_fill
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_transform
|
tuple[Union[NoneValueType, tuple[Transformation]]] | None
|
|
None
|
subunits_filter
|
tuple[Union[NoneValueType, Filter]] | None
|
|
None
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
n
|
int
|
|
1
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
830 831 832 833 834 835 836 837 838 839 840 841 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/core.py
719 720 721 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
711 712 713 714 715 716 717 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
723 724 725 726 727 728 729 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/core.py
691 692 693 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
703 704 705 706 707 708 709 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
695 696 697 698 699 700 701 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
683 684 685 686 687 688 689 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
675 676 677 678 679 680 681 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/core.py
747 748 749 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
731 732 733 734 735 736 737 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
739 740 741 742 743 744 745 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
751 752 753 754 755 756 757 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
759 760 761 762 763 764 765 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/core.py
775 776 777 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
779 780 781 782 783 784 785 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
767 768 769 770 771 772 773 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
Dissociation
dataclass
Dissociation(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
reversible: bool,
compartment: Compartment | None = None,
reactants: frozenset[Reactant] = frozenset(),
products: frozenset[Product] = frozenset(),
modifiers: frozenset[
Modulator | UnknownModulator
] = frozenset()
)
Bases: Reaction
Class for dissociations
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'3622f82a-5da8-46da-bd09-9459b7b28169'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
reversible
|
bool
|
|
required |
compartment
|
Compartment | None
|
|
None
|
DissociationLayout
dataclass
DissociationLayout(
*,
_left_connector_fraction: float = 0.4,
_right_connector_fraction: float = 0.6,
reaction_node_height: float = 10.0,
reaction_node_width: float = 10.0,
reaction_node_segment: int = 1,
reaction_node_stroke: (
NoneValueType | Color | None
) = black,
reaction_node_stroke_width: float | None = 1.0,
reaction_node_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
reaction_node_stroke_dashoffset: float | None = None,
reaction_node_fill: (
NoneValueType | Color | None
) = white,
reaction_node_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
reaction_node_filter: (
NoneValueType | Filter | None
) = None,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 2.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 2.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_arrowhead_fill: (
NoneValueType | Color | None
) = white,
end_arrowhead_filter: (
NoneValueType | Filter | None
) = None,
end_arrowhead_stroke: (
NoneValueType | Color | None
) = black,
end_arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
end_arrowhead_stroke_dashoffset: float | None = None,
end_arrowhead_stroke_width: float | None = 1.0,
end_arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
start_arrowhead_fill: (
NoneValueType | Color | None
) = black,
start_arrowhead_filter: (
NoneValueType | Filter | None
) = None,
start_arrowhead_stroke: (
NoneValueType | Color | None
) = black,
start_arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
start_arrowhead_stroke_dashoffset: float | None = None,
start_arrowhead_stroke_width: float | None = 1.0,
start_arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
reversible: bool = False,
end_arrowhead_height: float = 10.0,
end_arrowhead_sep: float = 2.0,
end_arrowhead_width: float = 10.0,
start_arrowhead_height: float = 8.0,
start_arrowhead_width: float = 15.0
)
Bases: _ReactionLayout, _ReactionNodeMixin
Class for dissociation layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
_left_connector_fraction
|
float
|
|
0.4
|
_right_connector_fraction
|
float
|
|
0.6
|
reaction_node_height
|
float
|
|
10.0
|
reaction_node_width
|
float
|
|
10.0
|
reaction_node_segment
|
int
|
|
1
|
reaction_node_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
reaction_node_stroke_width
|
float | None
|
|
1.0
|
reaction_node_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
reaction_node_stroke_dashoffset
|
float | None
|
|
None
|
reaction_node_fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
reaction_node_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
reaction_node_filter
|
NoneValueType | Filter | None
|
|
None
|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'd40d1f64-5d56-4fb5-a13e-b796cb72e13d'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
|
2.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The path stroke dasharray of the arc |
None
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
|
2.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
end_arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
end_arrowhead_filter
|
NoneValueType | Filter | None
|
|
None
|
end_arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
end_arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
end_arrowhead_stroke_dashoffset
|
float | None
|
|
None
|
end_arrowhead_stroke_width
|
float | None
|
|
1.0
|
end_arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
start_arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
start_arrowhead_filter
|
NoneValueType | Filter | None
|
|
None
|
start_arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
start_arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
start_arrowhead_stroke_dashoffset
|
float | None
|
|
None
|
start_arrowhead_stroke_width
|
float | None
|
|
1.0
|
start_arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
reversible
|
bool
|
|
False
|
end_arrowhead_height
|
float
|
|
10.0
|
end_arrowhead_sep
|
float
|
|
2.0
|
end_arrowhead_width
|
float
|
|
10.0
|
start_arrowhead_height
|
float
|
|
8.0
|
start_arrowhead_width
|
float
|
|
15.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_arrowhead_base |
Return the base anchor point of the double-headed arc end arrowhead |
end_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
end_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. |
end_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc end arrowhead |
end_arrowhead_length |
Return the length of the double-headed arc end arrowhead |
end_arrowhead_tip |
Return the tip anchor point of the double-headed arc end arrowhead |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the double-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_arrowhead_base |
Return the base anchor point of the double-headed arc start arrowhead |
start_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
start_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. |
start_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc start arrowhead |
start_arrowhead_length |
Return the length of the double-headed arc start arrowhead |
start_arrowhead_tip |
Return the tip anchor point of the double-headed arc start arrowhead |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_arrowhead_base
end_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 | |
end_arrowhead_bbox
end_arrowhead_bbox()
Return the bounding box of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1400 1401 1402 1403 1404 | |
end_arrowhead_border
end_arrowhead_border(point)
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 | |
end_arrowhead_drawing_elements
end_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 | |
end_arrowhead_length
end_arrowhead_length() -> float
Return the length of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1370 1371 1372 1373 1374 1375 1376 1377 | |
end_arrowhead_tip
end_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1379 1380 1381 1382 1383 1384 1385 1386 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the double-headed arc path
Source code in src/momapy/core.py
1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
Source code in src/momapy/celldesigner/core.py
793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_arrowhead_base
start_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 | |
start_arrowhead_bbox
start_arrowhead_bbox() -> Bbox
Return the bounding box of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1353 1354 1355 1356 1357 | |
start_arrowhead_border
start_arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 | |
start_arrowhead_drawing_elements
start_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 | |
start_arrowhead_length
start_arrowhead_length() -> float
Return the length of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1321 1322 1323 1324 1325 1326 1327 1328 | |
start_arrowhead_tip
start_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1330 1331 1332 1333 1334 1335 1336 1337 1338 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
Drug
dataclass
Drug(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
compartment: Compartment | None = None,
hypothetical: bool = False,
active: bool = False,
homomultimer: int = 1
)
Bases: Species
Class for drugs
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'e3da7cdf-55a1-48bc-b5c6-7e422d6719f7'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
compartment
|
Compartment | None
|
|
None
|
hypothetical
|
bool
|
Whether the species is hypothetical or not |
False
|
active
|
bool
|
Whether the species is active or not |
False
|
homomultimer
|
int
|
The number of subunits forming the species |
1
|
DrugLayout
dataclass
DrugLayout(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
offset: float = 3.0,
subunits_stroke: (
tuple[NoneValueType | Color] | None
) = None,
subunits_stroke_width: (
tuple[NoneValueType | float] | None
) = None,
subunits_stroke_dasharray: (
tuple[NoneValueType | tuple[float]] | None
) = None,
subunits_stroke_dashoffset: tuple[float] | None = None,
subunits_fill: (
tuple[NoneValueType | Color] | None
) = None,
subunits_transform: (
tuple[NoneValueType | tuple[Transformation]] | None
) = None,
subunits_filter: (
tuple[NoneValueType | Filter] | None
) = None,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float = 30.0,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 60.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
n: int = 1,
horizontal_proportion: float = 0.2,
sep: float = 4.0
)
Bases: _MultiNodeMixin, CellDesignerNode
Class for drug layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'743950d7-e028-436a-a080-d176f2495d6b'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
30.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
60.0
|
offset
|
float
|
|
3.0
|
subunits_stroke
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_stroke_width
|
tuple[Union[NoneValueType, float]] | None
|
|
None
|
subunits_stroke_dasharray
|
tuple[Union[NoneValueType, tuple[float]]] | None
|
|
None
|
subunits_stroke_dashoffset
|
tuple[float] | None
|
|
None
|
subunits_fill
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_transform
|
tuple[Union[NoneValueType, tuple[Transformation]]] | None
|
|
None
|
subunits_filter
|
tuple[Union[NoneValueType, Filter]] | None
|
|
None
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
n
|
int
|
|
1
|
horizontal_proportion
|
float
|
|
0.2
|
sep
|
float
|
|
4.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
830 831 832 833 834 835 836 837 838 839 840 841 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/core.py
719 720 721 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
711 712 713 714 715 716 717 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
723 724 725 726 727 728 729 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/core.py
691 692 693 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
703 704 705 706 707 708 709 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
695 696 697 698 699 700 701 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
683 684 685 686 687 688 689 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
675 676 677 678 679 680 681 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/core.py
747 748 749 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
731 732 733 734 735 736 737 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
739 740 741 742 743 744 745 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
751 752 753 754 755 756 757 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
759 760 761 762 763 764 765 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/core.py
775 776 777 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
779 780 781 782 783 784 785 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
767 768 769 770 771 772 773 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
Gene
dataclass
Gene(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
compartment: Compartment | None = None,
hypothetical: bool = False,
active: bool = False,
homomultimer: int = 1,
template: GeneTemplate,
modifications: frozenset[Modification] = frozenset()
)
Bases: Species
Class for genes
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'f030bb2b-037a-48c9-9e0f-b1fcd92813d1'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
compartment
|
Compartment | None
|
|
None
|
hypothetical
|
bool
|
Whether the species is hypothetical or not |
False
|
active
|
bool
|
Whether the species is active or not |
False
|
homomultimer
|
int
|
The number of subunits forming the species |
1
|
template
|
GeneTemplate
|
|
required |
GeneLayout
dataclass
GeneLayout(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
offset: float = 3.0,
subunits_stroke: (
tuple[NoneValueType | Color] | None
) = None,
subunits_stroke_width: (
tuple[NoneValueType | float] | None
) = None,
subunits_stroke_dasharray: (
tuple[NoneValueType | tuple[float]] | None
) = None,
subunits_stroke_dashoffset: tuple[float] | None = None,
subunits_fill: (
tuple[NoneValueType | Color] | None
) = None,
subunits_transform: (
tuple[NoneValueType | tuple[Transformation]] | None
) = None,
subunits_filter: (
tuple[NoneValueType | Filter] | None
) = None,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float = 30.0,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 60.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
n: int = 1
)
Bases: _MultiNodeMixin, CellDesignerNode
Class for gene layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'a2ccd3ad-16df-4927-a31b-cad1b8adbc43'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
30.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
60.0
|
offset
|
float
|
|
3.0
|
subunits_stroke
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_stroke_width
|
tuple[Union[NoneValueType, float]] | None
|
|
None
|
subunits_stroke_dasharray
|
tuple[Union[NoneValueType, tuple[float]]] | None
|
|
None
|
subunits_stroke_dashoffset
|
tuple[float] | None
|
|
None
|
subunits_fill
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_transform
|
tuple[Union[NoneValueType, tuple[Transformation]]] | None
|
|
None
|
subunits_filter
|
tuple[Union[NoneValueType, Filter]] | None
|
|
None
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
n
|
int
|
|
1
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
830 831 832 833 834 835 836 837 838 839 840 841 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/core.py
719 720 721 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
711 712 713 714 715 716 717 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
723 724 725 726 727 728 729 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/core.py
691 692 693 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
703 704 705 706 707 708 709 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
695 696 697 698 699 700 701 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
683 684 685 686 687 688 689 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
675 676 677 678 679 680 681 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/core.py
747 748 749 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
731 732 733 734 735 736 737 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
739 740 741 742 743 744 745 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
751 752 753 754 755 756 757 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
759 760 761 762 763 764 765 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/core.py
775 776 777 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
779 780 781 782 783 784 785 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
767 768 769 770 771 772 773 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
GeneTemplate
dataclass
GeneTemplate(
*,
id_: str = get_uuid4_as_str(),
name: str,
regions: frozenset[
ModificationSite
| CodingRegion
| RegulatoryRegion
| TranscriptionStartingSiteL
| TranscriptionStartingSiteR
] = frozenset()
)
Bases: SpeciesTemplate
Class for gene templates
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'48ae88dc-0eea-4978-8e60-5525c08b6711'
|
name
|
str
|
The name of the species template |
required |
GenericProtein
dataclass
GenericProtein(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
compartment: Compartment | None = None,
hypothetical: bool = False,
active: bool = False,
homomultimer: int = 1,
template: GenericProteinTemplate,
modifications: frozenset[Modification] = frozenset(),
structural_states: frozenset[
StructuralState
] = frozenset()
)
Bases: Protein
Class for generic proteins
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'9bc3515e-aca9-4a7a-9941-4953b17c0751'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
compartment
|
Compartment | None
|
|
None
|
hypothetical
|
bool
|
Whether the species is hypothetical or not |
False
|
active
|
bool
|
Whether the species is active or not |
False
|
homomultimer
|
int
|
The number of subunits forming the species |
1
|
template
|
GenericProteinTemplate
|
The template of the generic protein |
required |
GenericProteinLayout
dataclass
GenericProteinLayout(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
offset: float = 3.0,
subunits_stroke: (
tuple[NoneValueType | Color] | None
) = None,
subunits_stroke_width: (
tuple[NoneValueType | float] | None
) = None,
subunits_stroke_dasharray: (
tuple[NoneValueType | tuple[float]] | None
) = None,
subunits_stroke_dashoffset: tuple[float] | None = None,
subunits_fill: (
tuple[NoneValueType | Color] | None
) = None,
subunits_transform: (
tuple[NoneValueType | tuple[Transformation]] | None
) = None,
subunits_filter: (
tuple[NoneValueType | Filter] | None
) = None,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float = 30.0,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 60.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
n: int = 1,
rounded_corners: float = 5.0
)
Bases: _MultiNodeMixin, CellDesignerNode
Class for generic protein layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'31262bab-6731-46e3-b42b-dfc2373c2e91'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
30.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
60.0
|
offset
|
float
|
|
3.0
|
subunits_stroke
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_stroke_width
|
tuple[Union[NoneValueType, float]] | None
|
|
None
|
subunits_stroke_dasharray
|
tuple[Union[NoneValueType, tuple[float]]] | None
|
|
None
|
subunits_stroke_dashoffset
|
tuple[float] | None
|
|
None
|
subunits_fill
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_transform
|
tuple[Union[NoneValueType, tuple[Transformation]]] | None
|
|
None
|
subunits_filter
|
tuple[Union[NoneValueType, Filter]] | None
|
|
None
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
n
|
int
|
|
1
|
rounded_corners
|
float
|
|
5.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
830 831 832 833 834 835 836 837 838 839 840 841 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/core.py
719 720 721 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
711 712 713 714 715 716 717 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
723 724 725 726 727 728 729 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/core.py
691 692 693 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
703 704 705 706 707 708 709 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
695 696 697 698 699 700 701 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
683 684 685 686 687 688 689 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
675 676 677 678 679 680 681 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/core.py
747 748 749 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
731 732 733 734 735 736 737 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
739 740 741 742 743 744 745 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
751 752 753 754 755 756 757 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
759 760 761 762 763 764 765 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/core.py
775 776 777 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
779 780 781 782 783 784 785 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
767 768 769 770 771 772 773 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
GenericProteinTemplate
dataclass
GenericProteinTemplate(
*,
id_: str = get_uuid4_as_str(),
name: str,
modification_residues: frozenset[
ModificationResidue
] = frozenset()
)
Bases: ProteinTemplate
Class for generic protein templates
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'28797ef8-8412-49cb-8c94-b04ad136a7a1'
|
name
|
str
|
The name of the species template |
required |
HeterodimerAssociation
dataclass
HeterodimerAssociation(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
reversible: bool,
compartment: Compartment | None = None,
reactants: frozenset[Reactant] = frozenset(),
products: frozenset[Product] = frozenset(),
modifiers: frozenset[
Modulator | UnknownModulator
] = frozenset()
)
Bases: Reaction
Class for heterodimer associations
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'e9a1e01a-ba43-4438-a533-54da44968141'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
reversible
|
bool
|
|
required |
compartment
|
Compartment | None
|
|
None
|
HeterodimerAssociationLayout
dataclass
HeterodimerAssociationLayout(
*,
_left_connector_fraction: float = 0.4,
_right_connector_fraction: float = 0.6,
reaction_node_height: float = 10.0,
reaction_node_width: float = 10.0,
reaction_node_segment: int = 1,
reaction_node_stroke: (
NoneValueType | Color | None
) = black,
reaction_node_stroke_width: float | None = 1.0,
reaction_node_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
reaction_node_stroke_dashoffset: float | None = None,
reaction_node_fill: (
NoneValueType | Color | None
) = white,
reaction_node_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
reaction_node_filter: (
NoneValueType | Filter | None
) = None,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 2.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 2.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_arrowhead_fill: (
NoneValueType | Color | None
) = black,
end_arrowhead_filter: (
NoneValueType | Filter | None
) = None,
end_arrowhead_stroke: (
NoneValueType | Color | None
) = black,
end_arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
end_arrowhead_stroke_dashoffset: float | None = None,
end_arrowhead_stroke_width: float | None = 1.0,
end_arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
start_arrowhead_fill: (
NoneValueType | Color | None
) = black,
start_arrowhead_filter: (
NoneValueType | Filter | None
) = None,
start_arrowhead_stroke: (
NoneValueType | Color | None
) = black,
start_arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
start_arrowhead_stroke_dashoffset: float | None = None,
start_arrowhead_stroke_width: float | None = 1.0,
start_arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
reversible: bool = False,
end_arrowhead_height: float = 8.0,
end_arrowhead_width: float = 15.0,
start_arrowhead_height: float = 6.0,
start_arrowhead_width: float = 6.0
)
Bases: _ReactionLayout, _ReactionNodeMixin
Class for heterodimer association layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
_left_connector_fraction
|
float
|
|
0.4
|
_right_connector_fraction
|
float
|
|
0.6
|
reaction_node_height
|
float
|
|
10.0
|
reaction_node_width
|
float
|
|
10.0
|
reaction_node_segment
|
int
|
|
1
|
reaction_node_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
reaction_node_stroke_width
|
float | None
|
|
1.0
|
reaction_node_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
reaction_node_stroke_dashoffset
|
float | None
|
|
None
|
reaction_node_fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
reaction_node_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
reaction_node_filter
|
NoneValueType | Filter | None
|
|
None
|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'4f238607-d49a-434a-968d-4405b7537c47'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
|
2.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The path stroke dasharray of the arc |
None
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
|
2.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
end_arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
end_arrowhead_filter
|
NoneValueType | Filter | None
|
|
None
|
end_arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
end_arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
end_arrowhead_stroke_dashoffset
|
float | None
|
|
None
|
end_arrowhead_stroke_width
|
float | None
|
|
1.0
|
end_arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
start_arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
start_arrowhead_filter
|
NoneValueType | Filter | None
|
|
None
|
start_arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
start_arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
start_arrowhead_stroke_dashoffset
|
float | None
|
|
None
|
start_arrowhead_stroke_width
|
float | None
|
|
1.0
|
start_arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
reversible
|
bool
|
|
False
|
end_arrowhead_height
|
float
|
|
8.0
|
end_arrowhead_width
|
float
|
|
15.0
|
start_arrowhead_height
|
float
|
|
6.0
|
start_arrowhead_width
|
float
|
|
6.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_arrowhead_base |
Return the base anchor point of the double-headed arc end arrowhead |
end_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
end_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. |
end_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc end arrowhead |
end_arrowhead_length |
Return the length of the double-headed arc end arrowhead |
end_arrowhead_tip |
Return the tip anchor point of the double-headed arc end arrowhead |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the double-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_arrowhead_base |
Return the base anchor point of the double-headed arc start arrowhead |
start_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
start_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. |
start_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc start arrowhead |
start_arrowhead_length |
Return the length of the double-headed arc start arrowhead |
start_arrowhead_tip |
Return the tip anchor point of the double-headed arc start arrowhead |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_arrowhead_base
end_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 | |
end_arrowhead_bbox
end_arrowhead_bbox()
Return the bounding box of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1400 1401 1402 1403 1404 | |
end_arrowhead_border
end_arrowhead_border(point)
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 | |
end_arrowhead_drawing_elements
end_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 | |
end_arrowhead_length
end_arrowhead_length() -> float
Return the length of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1370 1371 1372 1373 1374 1375 1376 1377 | |
end_arrowhead_tip
end_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1379 1380 1381 1382 1383 1384 1385 1386 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the double-headed arc path
Source code in src/momapy/core.py
1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
Source code in src/momapy/celldesigner/core.py
793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_arrowhead_base
start_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 | |
start_arrowhead_bbox
start_arrowhead_bbox() -> Bbox
Return the bounding box of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1353 1354 1355 1356 1357 | |
start_arrowhead_border
start_arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 | |
start_arrowhead_drawing_elements
start_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 | |
start_arrowhead_length
start_arrowhead_length() -> float
Return the length of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1321 1322 1323 1324 1325 1326 1327 1328 | |
start_arrowhead_tip
start_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1330 1331 1332 1333 1334 1335 1336 1337 1338 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
Inhibition
dataclass
Inhibition(
*,
id_: str = get_uuid4_as_str(),
source: Species | BooleanLogicGate,
target: Species | None
)
Bases: Modulation
Class for inhibitions
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'a6ec452b-ffa1-4385-81ca-f3688fd7bafe'
|
source
|
Species | BooleanLogicGate
|
The source of the influence |
required |
target
|
Species | None
|
The target of the influence |
required |
InhibitionLayout
dataclass
InhibitionLayout(
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 3.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 0.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_fill: NoneValueType | Color | None = None,
arrowhead_filter: NoneValueType | Filter | None = None,
arrowhead_stroke: NoneValueType | Color | None = black,
arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
arrowhead_stroke_dashoffset: float | None = None,
arrowhead_stroke_width: float | None = 1.0,
arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_height: float = 10.0
)
Bases: CellDesignerSingleHeadedArc
Class for inhibition layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'd7407998-d5f8-440b-af8a-434b9c0fe181'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
|
3.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The path stroke dasharray of the arc |
None
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
The length the start of the arc will be shorten by |
0.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
arrowhead_fill
|
NoneValueType | Color | None
|
The arrowhead fill color of the arc |
None
|
arrowhead_filter
|
NoneValueType | Filter | None
|
The arrowhead filter of the arc |
None
|
arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The arrowhead stroke dasharray of the arc |
None
|
arrowhead_stroke_dashoffset
|
float | None
|
The arrowhead stroke dashoffset of the arc |
None
|
arrowhead_stroke_width
|
float | None
|
|
1.0
|
arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
The arrowhead transform of the arc |
None
|
arrowhead_height
|
float
|
|
10.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
1089 1090 1091 1092 1093 1094 1095 1096 1097 | |
arrowhead_bbox
arrowhead_bbox() -> Bbox
Return the bounding box of the single-headed arc arrowhead
Source code in src/momapy/core.py
1099 1100 1101 1102 1103 | |
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 | |
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 | |
arrowhead_length
arrowhead_length() -> float
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
1071 1072 1073 1074 1075 1076 1077 1078 | |
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
1080 1081 1082 1083 1084 1085 1086 1087 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
Inhibitor
dataclass
Inhibitor(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
referred_species: Species | BooleanLogicGate
)
Bases: Modulator
Class for inhibitors
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'c099381c-9637-4b51-98cd-57154b9b21e7'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
referred_species
|
Species | BooleanLogicGate
|
The species the modifier refers to |
required |
Ion
dataclass
Ion(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
compartment: Compartment | None = None,
hypothetical: bool = False,
active: bool = False,
homomultimer: int = 1
)
Bases: Species
Class for ions
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'2be4f1cd-eee6-489d-916b-89a755f2701f'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
compartment
|
Compartment | None
|
|
None
|
hypothetical
|
bool
|
Whether the species is hypothetical or not |
False
|
active
|
bool
|
Whether the species is active or not |
False
|
homomultimer
|
int
|
The number of subunits forming the species |
1
|
IonChannel
dataclass
IonChannel(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
compartment: Compartment | None = None,
hypothetical: bool = False,
active: bool = False,
homomultimer: int = 1,
template: IonChannelTemplate,
modifications: frozenset[Modification] = frozenset(),
structural_states: frozenset[
StructuralState
] = frozenset()
)
Bases: Protein
Class for ion channels
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'33283e2a-c906-4588-b9ee-b88579b3421f'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
compartment
|
Compartment | None
|
|
None
|
hypothetical
|
bool
|
Whether the species is hypothetical or not |
False
|
active
|
bool
|
Whether the species is active or not |
False
|
homomultimer
|
int
|
The number of subunits forming the species |
1
|
template
|
IonChannelTemplate
|
The template of the ion channel |
required |
IonChannelLayout
dataclass
IonChannelLayout(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
offset: float = 3.0,
subunits_stroke: (
tuple[NoneValueType | Color] | None
) = None,
subunits_stroke_width: (
tuple[NoneValueType | float] | None
) = None,
subunits_stroke_dasharray: (
tuple[NoneValueType | tuple[float]] | None
) = None,
subunits_stroke_dashoffset: tuple[float] | None = None,
subunits_fill: (
tuple[NoneValueType | Color] | None
) = None,
subunits_transform: (
tuple[NoneValueType | tuple[Transformation]] | None
) = None,
subunits_filter: (
tuple[NoneValueType | Filter] | None
) = None,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float = 30.0,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 60.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
n: int = 1,
rounded_corners: float = 5.0,
right_rectangle_width: float = 20.0
)
Bases: _MultiNodeMixin, CellDesignerNode
Class for generic ion channel layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'1d485eed-8b71-4ea8-944f-d40d1fff84cb'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
30.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
60.0
|
offset
|
float
|
|
3.0
|
subunits_stroke
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_stroke_width
|
tuple[Union[NoneValueType, float]] | None
|
|
None
|
subunits_stroke_dasharray
|
tuple[Union[NoneValueType, tuple[float]]] | None
|
|
None
|
subunits_stroke_dashoffset
|
tuple[float] | None
|
|
None
|
subunits_fill
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_transform
|
tuple[Union[NoneValueType, tuple[Transformation]]] | None
|
|
None
|
subunits_filter
|
tuple[Union[NoneValueType, Filter]] | None
|
|
None
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
n
|
int
|
|
1
|
rounded_corners
|
float
|
|
5.0
|
right_rectangle_width
|
float
|
|
20.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
830 831 832 833 834 835 836 837 838 839 840 841 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/core.py
719 720 721 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
711 712 713 714 715 716 717 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
723 724 725 726 727 728 729 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/core.py
691 692 693 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
703 704 705 706 707 708 709 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
695 696 697 698 699 700 701 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
683 684 685 686 687 688 689 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
675 676 677 678 679 680 681 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/core.py
747 748 749 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
731 732 733 734 735 736 737 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
739 740 741 742 743 744 745 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
751 752 753 754 755 756 757 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
759 760 761 762 763 764 765 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/core.py
775 776 777 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
779 780 781 782 783 784 785 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
767 768 769 770 771 772 773 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
IonChannelTemplate
dataclass
IonChannelTemplate(
*,
id_: str = get_uuid4_as_str(),
name: str,
modification_residues: frozenset[
ModificationResidue
] = frozenset()
)
Bases: ProteinTemplate
Class for ion channel templates
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'24bd17d0-ab6f-45db-a66d-b047ab718940'
|
name
|
str
|
The name of the species template |
required |
IonLayout
dataclass
IonLayout(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
offset: float = 3.0,
subunits_stroke: (
tuple[NoneValueType | Color] | None
) = None,
subunits_stroke_width: (
tuple[NoneValueType | float] | None
) = None,
subunits_stroke_dasharray: (
tuple[NoneValueType | tuple[float]] | None
) = None,
subunits_stroke_dashoffset: tuple[float] | None = None,
subunits_fill: (
tuple[NoneValueType | Color] | None
) = None,
subunits_transform: (
tuple[NoneValueType | tuple[Transformation]] | None
) = None,
subunits_filter: (
tuple[NoneValueType | Filter] | None
) = None,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float = 30.0,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 60.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
n: int = 1
)
Bases: _MultiNodeMixin, CellDesignerNode
Class for ion layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'a0493a62-c46f-44f1-8c3f-c131642752a4'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
30.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
60.0
|
offset
|
float
|
|
3.0
|
subunits_stroke
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_stroke_width
|
tuple[Union[NoneValueType, float]] | None
|
|
None
|
subunits_stroke_dasharray
|
tuple[Union[NoneValueType, tuple[float]]] | None
|
|
None
|
subunits_stroke_dashoffset
|
tuple[float] | None
|
|
None
|
subunits_fill
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_transform
|
tuple[Union[NoneValueType, tuple[Transformation]]] | None
|
|
None
|
subunits_filter
|
tuple[Union[NoneValueType, Filter]] | None
|
|
None
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
n
|
int
|
|
1
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
830 831 832 833 834 835 836 837 838 839 840 841 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/core.py
719 720 721 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
711 712 713 714 715 716 717 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
723 724 725 726 727 728 729 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/core.py
691 692 693 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
703 704 705 706 707 708 709 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
695 696 697 698 699 700 701 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
683 684 685 686 687 688 689 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
675 676 677 678 679 680 681 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/core.py
747 748 749 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
731 732 733 734 735 736 737 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
739 740 741 742 743 744 745 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
751 752 753 754 755 756 757 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
759 760 761 762 763 764 765 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/core.py
775 776 777 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
779 780 781 782 783 784 785 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
767 768 769 770 771 772 773 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
KnownTransitionOmitted
dataclass
KnownTransitionOmitted(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
reversible: bool,
compartment: Compartment | None = None,
reactants: frozenset[Reactant] = frozenset(),
products: frozenset[Product] = frozenset(),
modifiers: frozenset[
Modulator | UnknownModulator
] = frozenset()
)
Bases: Reaction
Class for known transitions omitted
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'3c267113-8b0a-4128-b498-f4525d27c3ae'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
reversible
|
bool
|
|
required |
compartment
|
Compartment | None
|
|
None
|
KnownTransitionOmittedLayout
dataclass
KnownTransitionOmittedLayout(
*,
_left_connector_fraction: float = 0.4,
_right_connector_fraction: float = 0.6,
reaction_node_height: float = 10.0,
reaction_node_width: float = 10.0,
reaction_node_segment: int = 1,
reaction_node_stroke: (
NoneValueType | Color | None
) = black,
reaction_node_stroke_width: float | None = 1.0,
reaction_node_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
reaction_node_stroke_dashoffset: float | None = None,
reaction_node_fill: (
NoneValueType | Color | None
) = white,
reaction_node_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
reaction_node_filter: (
NoneValueType | Filter | None
) = None,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 2.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 2.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_arrowhead_fill: (
NoneValueType | Color | None
) = black,
end_arrowhead_filter: (
NoneValueType | Filter | None
) = None,
end_arrowhead_stroke: (
NoneValueType | Color | None
) = black,
end_arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
end_arrowhead_stroke_dashoffset: float | None = None,
end_arrowhead_stroke_width: float | None = 1.0,
end_arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
start_arrowhead_fill: (
NoneValueType | Color | None
) = black,
start_arrowhead_filter: (
NoneValueType | Filter | None
) = None,
start_arrowhead_stroke: (
NoneValueType | Color | None
) = black,
start_arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
start_arrowhead_stroke_dashoffset: float | None = None,
start_arrowhead_stroke_width: float | None = 1.0,
start_arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
reversible: bool = False,
end_arrowhead_height: float = 8.0,
end_arrowhead_width: float = 15.0,
start_arrowhead_height: float = 8.0,
start_arrowhead_width: float = 15.0
)
Bases: _ReactionLayout, _ReactionNodeMixin
Class for known transition omitted layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
_left_connector_fraction
|
float
|
|
0.4
|
_right_connector_fraction
|
float
|
|
0.6
|
reaction_node_height
|
float
|
|
10.0
|
reaction_node_width
|
float
|
|
10.0
|
reaction_node_segment
|
int
|
|
1
|
reaction_node_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
reaction_node_stroke_width
|
float | None
|
|
1.0
|
reaction_node_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
reaction_node_stroke_dashoffset
|
float | None
|
|
None
|
reaction_node_fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
reaction_node_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
reaction_node_filter
|
NoneValueType | Filter | None
|
|
None
|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'0a27114f-98c1-43b4-a975-4adb30e77768'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
|
2.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The path stroke dasharray of the arc |
None
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
|
2.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
end_arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
end_arrowhead_filter
|
NoneValueType | Filter | None
|
|
None
|
end_arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
end_arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
end_arrowhead_stroke_dashoffset
|
float | None
|
|
None
|
end_arrowhead_stroke_width
|
float | None
|
|
1.0
|
end_arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
start_arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
start_arrowhead_filter
|
NoneValueType | Filter | None
|
|
None
|
start_arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
start_arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
start_arrowhead_stroke_dashoffset
|
float | None
|
|
None
|
start_arrowhead_stroke_width
|
float | None
|
|
1.0
|
start_arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
reversible
|
bool
|
|
False
|
end_arrowhead_height
|
float
|
|
8.0
|
end_arrowhead_width
|
float
|
|
15.0
|
start_arrowhead_height
|
float
|
|
8.0
|
start_arrowhead_width
|
float
|
|
15.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_arrowhead_base |
Return the base anchor point of the double-headed arc end arrowhead |
end_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
end_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. |
end_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc end arrowhead |
end_arrowhead_length |
Return the length of the double-headed arc end arrowhead |
end_arrowhead_tip |
Return the tip anchor point of the double-headed arc end arrowhead |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the double-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_arrowhead_base |
Return the base anchor point of the double-headed arc start arrowhead |
start_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
start_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. |
start_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc start arrowhead |
start_arrowhead_length |
Return the length of the double-headed arc start arrowhead |
start_arrowhead_tip |
Return the tip anchor point of the double-headed arc start arrowhead |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_arrowhead_base
end_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 | |
end_arrowhead_bbox
end_arrowhead_bbox()
Return the bounding box of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1400 1401 1402 1403 1404 | |
end_arrowhead_border
end_arrowhead_border(point)
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 | |
end_arrowhead_drawing_elements
end_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 | |
end_arrowhead_length
end_arrowhead_length() -> float
Return the length of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1370 1371 1372 1373 1374 1375 1376 1377 | |
end_arrowhead_tip
end_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1379 1380 1381 1382 1383 1384 1385 1386 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the double-headed arc path
Source code in src/momapy/core.py
1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
Source code in src/momapy/celldesigner/core.py
793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_arrowhead_base
start_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 | |
start_arrowhead_bbox
start_arrowhead_bbox() -> Bbox
Return the bounding box of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1353 1354 1355 1356 1357 | |
start_arrowhead_border
start_arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 | |
start_arrowhead_drawing_elements
start_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 | |
start_arrowhead_length
start_arrowhead_length() -> float
Return the length of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1321 1322 1323 1324 1325 1326 1327 1328 | |
start_arrowhead_tip
start_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1330 1331 1332 1333 1334 1335 1336 1337 1338 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
LogicArcLayout
dataclass
LogicArcLayout(
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 0.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 0.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_fill: NoneValueType | Color | None = None,
arrowhead_filter: NoneValueType | Filter | None = None,
arrowhead_stroke: NoneValueType | Color | None = black,
arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
arrowhead_stroke_dashoffset: float | None = None,
arrowhead_stroke_width: float | None = 1.0,
arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None
)
Bases: CellDesignerSingleHeadedArc
Class for logic arc layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'74ef6ef5-40af-407f-bbee-47fe49fe8625'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
The length the end of the arc will be shorten by |
0.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The path stroke dasharray of the arc |
None
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
The length the start of the arc will be shorten by |
0.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
arrowhead_fill
|
NoneValueType | Color | None
|
The arrowhead fill color of the arc |
None
|
arrowhead_filter
|
NoneValueType | Filter | None
|
The arrowhead filter of the arc |
None
|
arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The arrowhead stroke dasharray of the arc |
None
|
arrowhead_stroke_dashoffset
|
float | None
|
The arrowhead stroke dashoffset of the arc |
None
|
arrowhead_stroke_width
|
float | None
|
|
1.0
|
arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
The arrowhead transform of the arc |
None
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
1089 1090 1091 1092 1093 1094 1095 1096 1097 | |
arrowhead_bbox
arrowhead_bbox() -> Bbox
Return the bounding box of the single-headed arc arrowhead
Source code in src/momapy/core.py
1099 1100 1101 1102 1103 | |
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 | |
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 | |
arrowhead_length
arrowhead_length() -> float
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
1071 1072 1073 1074 1075 1076 1077 1078 | |
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
1080 1081 1082 1083 1084 1085 1086 1087 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
Modification
dataclass
Modification(
*,
id_: str = get_uuid4_as_str(),
residue: (
ModificationResidue | ModificationSite | None
) = None,
state: ModificationState | None = None
)
Bases: CellDesignerModelElement
Class for modifications
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'837000ca-de78-487f-b642-0e7a4e5ea4ed'
|
residue
|
ModificationResidue | ModificationSite | None
|
The residue of the modification |
None
|
state
|
ModificationState | None
|
The state of the modification |
None
|
ModificationLayout
dataclass
ModificationLayout(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float = 16.0,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 16.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None
)
Bases: _SimpleNodeMixin, CellDesignerNode
Class for modification layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'9a14e4cb-a3c6-4b26-bd56-4040c0edbb8b'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
16.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
16.0
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
label_center |
Return the label center anchor of the node |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
830 831 832 833 834 835 836 837 838 839 840 841 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/core.py
719 720 721 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
711 712 713 714 715 716 717 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
723 724 725 726 727 728 729 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
label_center
label_center() -> Point
Return the label center anchor of the node
Source code in src/momapy/core.py
791 792 793 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/core.py
691 692 693 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
703 704 705 706 707 708 709 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
695 696 697 698 699 700 701 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
683 684 685 686 687 688 689 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
675 676 677 678 679 680 681 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/core.py
747 748 749 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
731 732 733 734 735 736 737 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
739 740 741 742 743 744 745 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
751 752 753 754 755 756 757 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
759 760 761 762 763 764 765 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/core.py
775 776 777 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
779 780 781 782 783 784 785 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
767 768 769 770 771 772 773 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
ModificationResidue
dataclass
ModificationResidue(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
order: int | None = None
)
Bases: CellDesignerModelElement
Class for modification residues
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'd9ff4841-52be-40d4-8ffa-c75231aafa1b'
|
name
|
str | None
|
|
None
|
order
|
int | None
|
|
None
|
ModificationSite
dataclass
ModificationSite(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
active: bool = False
)
Bases: Region
Class for modification sites
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'cd22cd13-bba9-4a66-854c-cf6457f8eebd'
|
name
|
str | None
|
The name of the region |
None
|
active
|
bool
|
Whether the region is active or not |
False
|
ModificationState
Bases: Enum
Class for modification states
Modulation
dataclass
Modulation(
*,
id_: str = get_uuid4_as_str(),
source: Species | BooleanLogicGate,
target: Species | None
)
Bases: _Influence
Class for modulations
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'915110e5-9e9a-45fc-8f84-f7c2ec15afdf'
|
source
|
Species | BooleanLogicGate
|
The source of the influence |
required |
target
|
Species | None
|
The target of the influence |
required |
ModulationLayout
dataclass
ModulationLayout(
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 0.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 0.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_fill: NoneValueType | Color | None = white,
arrowhead_filter: NoneValueType | Filter | None = None,
arrowhead_stroke: NoneValueType | Color | None = black,
arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
arrowhead_stroke_dashoffset: float | None = None,
arrowhead_stroke_width: float | None = 1.0,
arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_height: float = 8.0,
arrowhead_width: float = 15.0
)
Bases: CellDesignerSingleHeadedArc
Class for modulation layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'32c9a431-0f6a-4770-b1ea-5ca24668e021'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
The length the end of the arc will be shorten by |
0.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The path stroke dasharray of the arc |
None
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
The length the start of the arc will be shorten by |
0.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
arrowhead_filter
|
NoneValueType | Filter | None
|
The arrowhead filter of the arc |
None
|
arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The arrowhead stroke dasharray of the arc |
None
|
arrowhead_stroke_dashoffset
|
float | None
|
The arrowhead stroke dashoffset of the arc |
None
|
arrowhead_stroke_width
|
float | None
|
|
1.0
|
arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
The arrowhead transform of the arc |
None
|
arrowhead_height
|
float
|
|
8.0
|
arrowhead_width
|
float
|
|
15.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
1089 1090 1091 1092 1093 1094 1095 1096 1097 | |
arrowhead_bbox
arrowhead_bbox() -> Bbox
Return the bounding box of the single-headed arc arrowhead
Source code in src/momapy/core.py
1099 1100 1101 1102 1103 | |
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 | |
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 | |
arrowhead_length
arrowhead_length() -> float
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
1071 1072 1073 1074 1075 1076 1077 1078 | |
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
1080 1081 1082 1083 1084 1085 1086 1087 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
Modulator
dataclass
Modulator(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
referred_species: Species | BooleanLogicGate
)
Bases: _Modifier
Class for modulators
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'e1fbf799-9f9e-4abe-bb96-2a8677a52e57'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
referred_species
|
Species | BooleanLogicGate
|
The species the modifier refers to |
required |
NegativeInfluence
dataclass
NegativeInfluence(
*,
id_: str = get_uuid4_as_str(),
source: Species | BooleanLogicGate,
target: Species | None
)
Bases: Modulation
Class for negative influences
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'03ab930b-0049-4fb3-960b-3bf61ce51528'
|
source
|
Species | BooleanLogicGate
|
The source of the influence |
required |
target
|
Species | None
|
The target of the influence |
required |
NotGate
dataclass
NotGate(
*,
id_: str = get_uuid4_as_str(),
inputs: frozenset[Species] = frozenset()
)
Bases: BooleanLogicGate
Class for not gates
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'80ebcbd5-dc3b-451d-902f-14e5a50cf842'
|
NotGateLayout
dataclass
NotGateLayout(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float = 15.0,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 15.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None
)
Bases: _SimpleNodeMixin, _TextMixin, CellDesignerNode
Class for not gate layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'65b7c8ad-bc66-45c1-b0bf-dc8064c17634'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
15.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
15.0
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
label_center |
Return the label center anchor of the node |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
830 831 832 833 834 835 836 837 838 839 840 841 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/core.py
719 720 721 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
711 712 713 714 715 716 717 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
723 724 725 726 727 728 729 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
label_center
label_center() -> Point
Return the label center anchor of the node
Source code in src/momapy/core.py
791 792 793 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/core.py
691 692 693 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
703 704 705 706 707 708 709 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
695 696 697 698 699 700 701 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
683 684 685 686 687 688 689 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
675 676 677 678 679 680 681 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/core.py
747 748 749 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
731 732 733 734 735 736 737 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
739 740 741 742 743 744 745 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
751 752 753 754 755 756 757 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
759 760 761 762 763 764 765 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/core.py
775 776 777 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
779 780 781 782 783 784 785 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
767 768 769 770 771 772 773 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
OrGate
dataclass
OrGate(
*,
id_: str = get_uuid4_as_str(),
inputs: frozenset[Species] = frozenset()
)
Bases: BooleanLogicGate
Class for or gates
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'26207812-ba21-4e72-a173-227b697a47eb'
|
OrGateLayout
dataclass
OrGateLayout(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float = 15.0,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 15.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None
)
Bases: _SimpleNodeMixin, _TextMixin, CellDesignerNode
Class for or gate layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'7c90bc81-b744-4678-9fc1-cfc043ed58db'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
15.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
15.0
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
label_center |
Return the label center anchor of the node |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
830 831 832 833 834 835 836 837 838 839 840 841 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/core.py
719 720 721 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
711 712 713 714 715 716 717 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
723 724 725 726 727 728 729 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
label_center
label_center() -> Point
Return the label center anchor of the node
Source code in src/momapy/core.py
791 792 793 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/core.py
691 692 693 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
703 704 705 706 707 708 709 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
695 696 697 698 699 700 701 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
683 684 685 686 687 688 689 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
675 676 677 678 679 680 681 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/core.py
747 748 749 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
731 732 733 734 735 736 737 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
739 740 741 742 743 744 745 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
751 752 753 754 755 756 757 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
759 760 761 762 763 764 765 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/core.py
775 776 777 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
779 780 781 782 783 784 785 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
767 768 769 770 771 772 773 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
OvalCompartmentLayout
dataclass
OvalCompartmentLayout(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float = 16.0,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 16.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
inner_fill: NoneValueType | Color | None = white,
inner_stroke: NoneValueType | Color | None = black,
inner_stroke_width: float | None = 1.0,
sep: float = 12.0
)
Bases: _SimpleNodeMixin, CellDesignerNode
Class for oval compartment layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'64b7f650-c44b-47ac-8f77-e68dc0709ea1'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
16.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
16.0
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
inner_fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
inner_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
inner_stroke_width
|
float | None
|
|
1.0
|
sep
|
float
|
|
12.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
label_center |
Return the label center anchor of the node |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
830 831 832 833 834 835 836 837 838 839 840 841 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/core.py
719 720 721 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
711 712 713 714 715 716 717 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
723 724 725 726 727 728 729 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
label_center
label_center() -> Point
Return the label center anchor of the node
Source code in src/momapy/core.py
791 792 793 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/core.py
691 692 693 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
703 704 705 706 707 708 709 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
695 696 697 698 699 700 701 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
683 684 685 686 687 688 689 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
675 676 677 678 679 680 681 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/core.py
747 748 749 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
731 732 733 734 735 736 737 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
739 740 741 742 743 744 745 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
751 752 753 754 755 756 757 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
759 760 761 762 763 764 765 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/core.py
775 776 777 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
779 780 781 782 783 784 785 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
767 768 769 770 771 772 773 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
Phenotype
dataclass
Phenotype(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
compartment: Compartment | None = None,
hypothetical: bool = False,
active: bool = False,
homomultimer: int = 1
)
Bases: Species
Class for phenotypes
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'7c38e877-6a87-4ebf-91d1-0fc82b8840b7'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
compartment
|
Compartment | None
|
|
None
|
hypothetical
|
bool
|
Whether the species is hypothetical or not |
False
|
active
|
bool
|
Whether the species is active or not |
False
|
homomultimer
|
int
|
The number of subunits forming the species |
1
|
PhenotypeLayout
dataclass
PhenotypeLayout(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
offset: float = 3.0,
subunits_stroke: (
tuple[NoneValueType | Color] | None
) = None,
subunits_stroke_width: (
tuple[NoneValueType | float] | None
) = None,
subunits_stroke_dasharray: (
tuple[NoneValueType | tuple[float]] | None
) = None,
subunits_stroke_dashoffset: tuple[float] | None = None,
subunits_fill: (
tuple[NoneValueType | Color] | None
) = None,
subunits_transform: (
tuple[NoneValueType | tuple[Transformation]] | None
) = None,
subunits_filter: (
tuple[NoneValueType | Filter] | None
) = None,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float = 30.0,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 60.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
n: int = 1,
angle: float = 60.0
)
Bases: _MultiNodeMixin, CellDesignerNode
Class for phenotype layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'1e67374d-9c74-48b4-b5e2-febfe4b68db3'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
30.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
60.0
|
offset
|
float
|
|
3.0
|
subunits_stroke
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_stroke_width
|
tuple[Union[NoneValueType, float]] | None
|
|
None
|
subunits_stroke_dasharray
|
tuple[Union[NoneValueType, tuple[float]]] | None
|
|
None
|
subunits_stroke_dashoffset
|
tuple[float] | None
|
|
None
|
subunits_fill
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_transform
|
tuple[Union[NoneValueType, tuple[Transformation]]] | None
|
|
None
|
subunits_filter
|
tuple[Union[NoneValueType, Filter]] | None
|
|
None
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
n
|
int
|
|
1
|
angle
|
float
|
|
60.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
angle |
float
|
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
class-attribute
instance-attribute
angle: float = 60.0
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/celldesigner/core.py
1283 1284 1285 1286 1287 1288 1289 1290 1291 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/celldesigner/core.py
1273 1274 1275 1276 1277 1278 1279 1280 1281 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/celldesigner/core.py
1293 1294 1295 1296 1297 1298 1299 1300 1301 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/celldesigner/core.py
1243 1244 1245 1246 1247 1248 1249 1250 1251 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/celldesigner/core.py
1263 1264 1265 1266 1267 1268 1269 1270 1271 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/celldesigner/core.py
1253 1254 1255 1256 1257 1258 1259 1260 1261 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/celldesigner/core.py
1233 1234 1235 1236 1237 1238 1239 1240 1241 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/celldesigner/core.py
1223 1224 1225 1226 1227 1228 1229 1230 1231 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/celldesigner/core.py
1323 1324 1325 1326 1327 1328 1329 1330 1331 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/celldesigner/core.py
1303 1304 1305 1306 1307 1308 1309 1310 1311 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/celldesigner/core.py
1313 1314 1315 1316 1317 1318 1319 1320 1321 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/celldesigner/core.py
1333 1334 1335 1336 1337 1338 1339 1340 1341 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/celldesigner/core.py
1343 1344 1345 1346 1347 1348 1349 1350 1351 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/celldesigner/core.py
1363 1364 1365 1366 1367 1368 1369 1370 1371 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/celldesigner/core.py
1373 1374 1375 1376 1377 1378 1379 1380 1381 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/celldesigner/core.py
1353 1354 1355 1356 1357 1358 1359 1360 1361 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
PhysicalStimulation
dataclass
PhysicalStimulation(
*,
id_: str = get_uuid4_as_str(),
source: Species | BooleanLogicGate,
target: Species | None
)
Bases: Modulation
Class for physical stimulations
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'ae22eb54-91e5-4872-b32b-98ecc6189452'
|
source
|
Species | BooleanLogicGate
|
The source of the influence |
required |
target
|
Species | None
|
The target of the influence |
required |
PhysicalStimulationLayout
dataclass
PhysicalStimulationLayout(
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 0.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 0.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_fill: NoneValueType | Color | None = white,
arrowhead_filter: NoneValueType | Filter | None = None,
arrowhead_stroke: NoneValueType | Color | None = black,
arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
arrowhead_stroke_dashoffset: float | None = None,
arrowhead_stroke_width: float | None = 1.0,
arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_height: float = 10.0,
arrowhead_width: float = 10.0
)
Bases: CellDesignerSingleHeadedArc
Class for physical stimulation layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'6d8ec003-fa2b-421d-ba42-8f3a170301ea'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
The length the end of the arc will be shorten by |
0.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The path stroke dasharray of the arc |
None
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
The length the start of the arc will be shorten by |
0.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
arrowhead_filter
|
NoneValueType | Filter | None
|
The arrowhead filter of the arc |
None
|
arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The arrowhead stroke dasharray of the arc |
None
|
arrowhead_stroke_dashoffset
|
float | None
|
The arrowhead stroke dashoffset of the arc |
None
|
arrowhead_stroke_width
|
float | None
|
|
1.0
|
arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
The arrowhead transform of the arc |
None
|
arrowhead_height
|
float
|
|
10.0
|
arrowhead_width
|
float
|
|
10.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
1089 1090 1091 1092 1093 1094 1095 1096 1097 | |
arrowhead_bbox
arrowhead_bbox() -> Bbox
Return the bounding box of the single-headed arc arrowhead
Source code in src/momapy/core.py
1099 1100 1101 1102 1103 | |
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 | |
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 | |
arrowhead_length
arrowhead_length() -> float
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
1071 1072 1073 1074 1075 1076 1077 1078 | |
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
1080 1081 1082 1083 1084 1085 1086 1087 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
PhysicalStimulator
dataclass
PhysicalStimulator(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
referred_species: Species | BooleanLogicGate
)
Bases: Modulator
Class for physical stimulators
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'3ebbddf6-4d1f-4f34-95ab-7c1e2b961bd0'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
referred_species
|
Species | BooleanLogicGate
|
The species the modifier refers to |
required |
PositiveInfluence
dataclass
PositiveInfluence(
*,
id_: str = get_uuid4_as_str(),
source: Species | BooleanLogicGate,
target: Species | None
)
Bases: Modulation
Class for positive influences
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'f4b9316f-a902-4daf-8d45-b5ee36c4886e'
|
source
|
Species | BooleanLogicGate
|
The source of the influence |
required |
target
|
Species | None
|
The target of the influence |
required |
PositiveInfluenceLayout
dataclass
PositiveInfluenceLayout(
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 0.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 0.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_fill: (
NoneValueType | Color | None
) = NoneValue,
arrowhead_filter: NoneValueType | Filter | None = None,
arrowhead_stroke: NoneValueType | Color | None = black,
arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
arrowhead_stroke_dashoffset: float | None = None,
arrowhead_stroke_width: float | None = 2.0,
arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_height: float = 10.0,
arrowhead_width: float = 10.0
)
Bases: CellDesignerSingleHeadedArc
Class for positive influence layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'1e05ab8d-b2f2-4761-a063-f319956ab324'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
The length the end of the arc will be shorten by |
0.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The path stroke dasharray of the arc |
None
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
The length the start of the arc will be shorten by |
0.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
arrowhead_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
arrowhead_filter
|
NoneValueType | Filter | None
|
The arrowhead filter of the arc |
None
|
arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The arrowhead stroke dasharray of the arc |
None
|
arrowhead_stroke_dashoffset
|
float | None
|
The arrowhead stroke dashoffset of the arc |
None
|
arrowhead_stroke_width
|
float | None
|
|
2.0
|
arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
The arrowhead transform of the arc |
None
|
arrowhead_height
|
float
|
|
10.0
|
arrowhead_width
|
float
|
|
10.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
1089 1090 1091 1092 1093 1094 1095 1096 1097 | |
arrowhead_bbox
arrowhead_bbox() -> Bbox
Return the bounding box of the single-headed arc arrowhead
Source code in src/momapy/core.py
1099 1100 1101 1102 1103 | |
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 | |
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 | |
arrowhead_length
arrowhead_length() -> float
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
1071 1072 1073 1074 1075 1076 1077 1078 | |
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
1080 1081 1082 1083 1084 1085 1086 1087 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
Product
dataclass
Product(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
referred_species: Species,
stoichiometry: int | None = None,
base: bool = False
)
Bases: SpeciesReference, CellDesignerModelElement
Class for products
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'1a5fa454-dbd9-4c26-97c5-f971e3c8487a'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
referred_species
|
Species
|
|
required |
stoichiometry
|
int | None
|
|
None
|
base
|
bool
|
Whether the product is a base product or not |
False
|
ProductionLayout
dataclass
ProductionLayout(
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 2.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 0.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_fill: NoneValueType | Color | None = black,
arrowhead_filter: NoneValueType | Filter | None = None,
arrowhead_stroke: NoneValueType | Color | None = black,
arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
arrowhead_stroke_dashoffset: float | None = None,
arrowhead_stroke_width: float | None = 1.0,
arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_height: float = 8.0,
arrowhead_width: float = 15.0
)
Bases: CellDesignerSingleHeadedArc
Class for production layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'f1a3ad8a-5957-4ad6-9b2f-dab73744f846'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
|
2.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The path stroke dasharray of the arc |
None
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
The length the start of the arc will be shorten by |
0.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
arrowhead_filter
|
NoneValueType | Filter | None
|
The arrowhead filter of the arc |
None
|
arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The arrowhead stroke dasharray of the arc |
None
|
arrowhead_stroke_dashoffset
|
float | None
|
The arrowhead stroke dashoffset of the arc |
None
|
arrowhead_stroke_width
|
float | None
|
|
1.0
|
arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
The arrowhead transform of the arc |
None
|
arrowhead_height
|
float
|
|
8.0
|
arrowhead_width
|
float
|
|
15.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
1089 1090 1091 1092 1093 1094 1095 1096 1097 | |
arrowhead_bbox
arrowhead_bbox() -> Bbox
Return the bounding box of the single-headed arc arrowhead
Source code in src/momapy/core.py
1099 1100 1101 1102 1103 | |
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 | |
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 | |
arrowhead_length
arrowhead_length() -> float
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
1071 1072 1073 1074 1075 1076 1077 1078 | |
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
1080 1081 1082 1083 1084 1085 1086 1087 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
Protein
dataclass
Protein(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
compartment: Compartment | None = None,
hypothetical: bool = False,
active: bool = False,
homomultimer: int = 1,
template: ProteinTemplate,
modifications: frozenset[Modification] = frozenset(),
structural_states: frozenset[
StructuralState
] = frozenset()
)
Bases: Species
Base class for proteins
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'177f2f1a-5bb4-45f7-94ae-00347ed2ce18'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
compartment
|
Compartment | None
|
|
None
|
hypothetical
|
bool
|
Whether the species is hypothetical or not |
False
|
active
|
bool
|
Whether the species is active or not |
False
|
homomultimer
|
int
|
The number of subunits forming the species |
1
|
template
|
ProteinTemplate
|
The template of the species |
required |
ProteinBindingDomain
dataclass
ProteinBindingDomain(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
active: bool = False
)
Bases: Region
Class for protein binding domains
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'552fbfe1-86fd-4584-ba50-97a86733632e'
|
name
|
str | None
|
The name of the region |
None
|
active
|
bool
|
Whether the region is active or not |
False
|
ProteinTemplate
dataclass
ProteinTemplate(
*,
id_: str = get_uuid4_as_str(),
name: str,
modification_residues: frozenset[
ModificationResidue
] = frozenset()
)
Bases: SpeciesTemplate
Base class for protein templates
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'942c668d-47d8-4ed1-b664-38f299d61406'
|
name
|
str
|
The name of the species template |
required |
RNA
dataclass
RNA(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
compartment: Compartment | None = None,
hypothetical: bool = False,
active: bool = False,
homomultimer: int = 1,
template: RNATemplate,
modifications: frozenset[Modification] = frozenset()
)
Bases: Species
Class for RNAs
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'51234b8e-53a6-44e4-a37f-b538278d9b00'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
compartment
|
Compartment | None
|
|
None
|
hypothetical
|
bool
|
Whether the species is hypothetical or not |
False
|
active
|
bool
|
Whether the species is active or not |
False
|
homomultimer
|
int
|
The number of subunits forming the species |
1
|
template
|
RNATemplate
|
|
required |
RNALayout
dataclass
RNALayout(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
offset: float = 3.0,
subunits_stroke: (
tuple[NoneValueType | Color] | None
) = None,
subunits_stroke_width: (
tuple[NoneValueType | float] | None
) = None,
subunits_stroke_dasharray: (
tuple[NoneValueType | tuple[float]] | None
) = None,
subunits_stroke_dashoffset: tuple[float] | None = None,
subunits_fill: (
tuple[NoneValueType | Color] | None
) = None,
subunits_transform: (
tuple[NoneValueType | tuple[Transformation]] | None
) = None,
subunits_filter: (
tuple[NoneValueType | Filter] | None
) = None,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float = 30.0,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 60.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
n: int = 1,
angle: float = 45.0
)
Bases: _MultiNodeMixin, CellDesignerNode
Class for RNA layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'8a152cde-bd47-4b33-af0e-0314d5bd9ea7'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
30.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
60.0
|
offset
|
float
|
|
3.0
|
subunits_stroke
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_stroke_width
|
tuple[Union[NoneValueType, float]] | None
|
|
None
|
subunits_stroke_dasharray
|
tuple[Union[NoneValueType, tuple[float]]] | None
|
|
None
|
subunits_stroke_dashoffset
|
tuple[float] | None
|
|
None
|
subunits_fill
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_transform
|
tuple[Union[NoneValueType, tuple[Transformation]]] | None
|
|
None
|
subunits_filter
|
tuple[Union[NoneValueType, Filter]] | None
|
|
None
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
n
|
int
|
|
1
|
angle
|
float
|
|
45.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
angle |
float
|
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
class-attribute
instance-attribute
angle: float = 45.0
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/celldesigner/core.py
1457 1458 1459 1460 1461 1462 1463 1464 1465 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/celldesigner/core.py
1447 1448 1449 1450 1451 1452 1453 1454 1455 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/celldesigner/core.py
1467 1468 1469 1470 1471 1472 1473 1474 1475 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/celldesigner/core.py
1417 1418 1419 1420 1421 1422 1423 1424 1425 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/celldesigner/core.py
1437 1438 1439 1440 1441 1442 1443 1444 1445 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/celldesigner/core.py
1427 1428 1429 1430 1431 1432 1433 1434 1435 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/celldesigner/core.py
1407 1408 1409 1410 1411 1412 1413 1414 1415 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/celldesigner/core.py
1397 1398 1399 1400 1401 1402 1403 1404 1405 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/celldesigner/core.py
1497 1498 1499 1500 1501 1502 1503 1504 1505 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/celldesigner/core.py
1477 1478 1479 1480 1481 1482 1483 1484 1485 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/celldesigner/core.py
1487 1488 1489 1490 1491 1492 1493 1494 1495 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/celldesigner/core.py
1507 1508 1509 1510 1511 1512 1513 1514 1515 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/celldesigner/core.py
1517 1518 1519 1520 1521 1522 1523 1524 1525 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/celldesigner/core.py
1537 1538 1539 1540 1541 1542 1543 1544 1545 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/celldesigner/core.py
1547 1548 1549 1550 1551 1552 1553 1554 1555 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/celldesigner/core.py
1527 1528 1529 1530 1531 1532 1533 1534 1535 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
RNATemplate
dataclass
RNATemplate(
*,
id_: str = get_uuid4_as_str(),
name: str,
regions: frozenset[
ModificationSite
| CodingRegion
| ProteinBindingDomain
] = frozenset()
)
Bases: SpeciesTemplate
Class for RNA templates
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'346ef718-1af9-4901-b08d-552b5c2c24da'
|
name
|
str
|
The name of the species template |
required |
Reactant
dataclass
Reactant(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
referred_species: Species,
stoichiometry: int | None = None,
base: bool = False
)
Bases: SpeciesReference, CellDesignerModelElement
Class for reactants
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'84acfab8-439c-42fe-9589-c4768f6a912f'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
referred_species
|
Species
|
|
required |
stoichiometry
|
int | None
|
|
None
|
base
|
bool
|
Whether the reactant is a base reactant or not |
False
|
Reaction
dataclass
Reaction(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
reversible: bool,
compartment: Compartment | None = None,
reactants: frozenset[Reactant] = frozenset(),
products: frozenset[Product] = frozenset(),
modifiers: frozenset[
Modulator | UnknownModulator
] = frozenset()
)
Bases: Reaction, CellDesignerModelElement
Base class for reactions
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'4c149794-7e00-42e2-994c-4ba370b84e63'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
reversible
|
bool
|
|
required |
compartment
|
Compartment | None
|
|
None
|
Receptor
dataclass
Receptor(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
compartment: Compartment | None = None,
hypothetical: bool = False,
active: bool = False,
homomultimer: int = 1,
template: ReceptorTemplate,
modifications: frozenset[Modification] = frozenset(),
structural_states: frozenset[
StructuralState
] = frozenset()
)
Bases: Protein
Class for receptors
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'0d475564-1eb6-4bbf-aa5d-f4bd25b24654'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
compartment
|
Compartment | None
|
|
None
|
hypothetical
|
bool
|
Whether the species is hypothetical or not |
False
|
active
|
bool
|
Whether the species is active or not |
False
|
homomultimer
|
int
|
The number of subunits forming the species |
1
|
template
|
ReceptorTemplate
|
The template of the receptor |
required |
ReceptorLayout
dataclass
ReceptorLayout(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
offset: float = 3.0,
subunits_stroke: (
tuple[NoneValueType | Color] | None
) = None,
subunits_stroke_width: (
tuple[NoneValueType | float] | None
) = None,
subunits_stroke_dasharray: (
tuple[NoneValueType | tuple[float]] | None
) = None,
subunits_stroke_dashoffset: tuple[float] | None = None,
subunits_fill: (
tuple[NoneValueType | Color] | None
) = None,
subunits_transform: (
tuple[NoneValueType | tuple[Transformation]] | None
) = None,
subunits_filter: (
tuple[NoneValueType | Filter] | None
) = None,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float = 30.0,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 60.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
n: int = 1,
vertical_truncation: float = 0.1
)
Bases: _MultiNodeMixin, CellDesignerNode
Class for receptor layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'68efcca7-5196-4c44-be93-438ed47374c4'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
30.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
60.0
|
offset
|
float
|
|
3.0
|
subunits_stroke
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_stroke_width
|
tuple[Union[NoneValueType, float]] | None
|
|
None
|
subunits_stroke_dasharray
|
tuple[Union[NoneValueType, tuple[float]]] | None
|
|
None
|
subunits_stroke_dashoffset
|
tuple[float] | None
|
|
None
|
subunits_fill
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_transform
|
tuple[Union[NoneValueType, tuple[Transformation]]] | None
|
|
None
|
subunits_filter
|
tuple[Union[NoneValueType, Filter]] | None
|
|
None
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
n
|
int
|
|
1
|
vertical_truncation
|
float
|
|
0.1
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
830 831 832 833 834 835 836 837 838 839 840 841 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/celldesigner/core.py
1927 1928 1929 1930 1931 1932 1933 1934 1935 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/celldesigner/core.py
1917 1918 1919 1920 1921 1922 1923 1924 1925 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/celldesigner/core.py
1937 1938 1939 1940 1941 1942 1943 1944 1945 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/celldesigner/core.py
1887 1888 1889 1890 1891 1892 1893 1894 1895 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/celldesigner/core.py
1907 1908 1909 1910 1911 1912 1913 1914 1915 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/celldesigner/core.py
1897 1898 1899 1900 1901 1902 1903 1904 1905 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/celldesigner/core.py
1877 1878 1879 1880 1881 1882 1883 1884 1885 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/celldesigner/core.py
1867 1868 1869 1870 1871 1872 1873 1874 1875 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/celldesigner/core.py
1967 1968 1969 1970 1971 1972 1973 1974 1975 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/celldesigner/core.py
1947 1948 1949 1950 1951 1952 1953 1954 1955 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/celldesigner/core.py
1957 1958 1959 1960 1961 1962 1963 1964 1965 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/celldesigner/core.py
1977 1978 1979 1980 1981 1982 1983 1984 1985 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/celldesigner/core.py
1987 1988 1989 1990 1991 1992 1993 1994 1995 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/celldesigner/core.py
2007 2008 2009 2010 2011 2012 2013 2014 2015 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/celldesigner/core.py
2017 2018 2019 2020 2021 2022 2023 2024 2025 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/celldesigner/core.py
1997 1998 1999 2000 2001 2002 2003 2004 2005 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
ReceptorTemplate
dataclass
ReceptorTemplate(
*,
id_: str = get_uuid4_as_str(),
name: str,
modification_residues: frozenset[
ModificationResidue
] = frozenset()
)
Bases: ProteinTemplate
Class for receptor templates
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'80bffc3b-c562-46a1-b03b-39a52711eecf'
|
name
|
str
|
The name of the species template |
required |
RectangleCompartmentLayout
dataclass
RectangleCompartmentLayout(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float = 16.0,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 16.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
inner_fill: NoneValueType | Color | None = white,
inner_rounded_corners: float = 10.0,
inner_stroke: NoneValueType | Color | None = black,
inner_stroke_width: float | None = 1.0,
rounded_corners: float = 10.0,
sep: float = 12.0
)
Bases: _SimpleNodeMixin, CellDesignerNode
Class for rectangle compartment layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'5901d709-2623-4988-821d-217d8f489bd9'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
16.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
16.0
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
inner_fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
inner_rounded_corners
|
float
|
|
10.0
|
inner_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
inner_stroke_width
|
float | None
|
|
1.0
|
rounded_corners
|
float
|
|
10.0
|
sep
|
float
|
|
12.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
label_center |
Return the label center anchor of the node |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
830 831 832 833 834 835 836 837 838 839 840 841 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/core.py
719 720 721 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
711 712 713 714 715 716 717 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
723 724 725 726 727 728 729 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
label_center
label_center() -> Point
Return the label center anchor of the node
Source code in src/momapy/core.py
791 792 793 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/core.py
691 692 693 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
703 704 705 706 707 708 709 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
695 696 697 698 699 700 701 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
683 684 685 686 687 688 689 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
675 676 677 678 679 680 681 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/core.py
747 748 749 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
731 732 733 734 735 736 737 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
739 740 741 742 743 744 745 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
751 752 753 754 755 756 757 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
759 760 761 762 763 764 765 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/core.py
775 776 777 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
779 780 781 782 783 784 785 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
767 768 769 770 771 772 773 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
Region
dataclass
Region(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
active: bool = False
)
Bases: CellDesignerModelElement
Class for regions
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'a2250210-ee1a-4aff-af1b-38235864aaa2'
|
name
|
str | None
|
The name of the region |
None
|
active
|
bool
|
Whether the region is active or not |
False
|
RegulatoryRegion
dataclass
RegulatoryRegion(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
active: bool = False
)
Bases: Region
Class for regulatory regions
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'5e058d47-f294-440d-9040-b95f51e4fc94'
|
name
|
str | None
|
The name of the region |
None
|
active
|
bool
|
Whether the region is active or not |
False
|
SimpleMolecule
dataclass
SimpleMolecule(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
compartment: Compartment | None = None,
hypothetical: bool = False,
active: bool = False,
homomultimer: int = 1
)
Bases: Species
Class for simple molecules
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'7e9cb318-fb00-4052-9f3f-74dff3c2bad6'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
compartment
|
Compartment | None
|
|
None
|
hypothetical
|
bool
|
Whether the species is hypothetical or not |
False
|
active
|
bool
|
Whether the species is active or not |
False
|
homomultimer
|
int
|
The number of subunits forming the species |
1
|
SimpleMoleculeLayout
dataclass
SimpleMoleculeLayout(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
offset: float = 3.0,
subunits_stroke: (
tuple[NoneValueType | Color] | None
) = None,
subunits_stroke_width: (
tuple[NoneValueType | float] | None
) = None,
subunits_stroke_dasharray: (
tuple[NoneValueType | tuple[float]] | None
) = None,
subunits_stroke_dashoffset: tuple[float] | None = None,
subunits_fill: (
tuple[NoneValueType | Color] | None
) = None,
subunits_transform: (
tuple[NoneValueType | tuple[Transformation]] | None
) = None,
subunits_filter: (
tuple[NoneValueType | Filter] | None
) = None,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float = 30.0,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 60.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
n: int = 1
)
Bases: _MultiNodeMixin, CellDesignerNode
Class for simple chemical layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'178ec587-2a1d-4527-a88f-dca259580bc9'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
30.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
60.0
|
offset
|
float
|
|
3.0
|
subunits_stroke
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_stroke_width
|
tuple[Union[NoneValueType, float]] | None
|
|
None
|
subunits_stroke_dasharray
|
tuple[Union[NoneValueType, tuple[float]]] | None
|
|
None
|
subunits_stroke_dashoffset
|
tuple[float] | None
|
|
None
|
subunits_fill
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_transform
|
tuple[Union[NoneValueType, tuple[Transformation]]] | None
|
|
None
|
subunits_filter
|
tuple[Union[NoneValueType, Filter]] | None
|
|
None
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
n
|
int
|
|
1
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
830 831 832 833 834 835 836 837 838 839 840 841 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/core.py
719 720 721 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
711 712 713 714 715 716 717 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
723 724 725 726 727 728 729 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/core.py
691 692 693 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
703 704 705 706 707 708 709 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
695 696 697 698 699 700 701 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
683 684 685 686 687 688 689 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
675 676 677 678 679 680 681 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/core.py
747 748 749 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
731 732 733 734 735 736 737 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
739 740 741 742 743 744 745 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
751 752 753 754 755 756 757 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
759 760 761 762 763 764 765 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/core.py
775 776 777 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
779 780 781 782 783 784 785 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
767 768 769 770 771 772 773 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
Species
dataclass
Species(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
compartment: Compartment | None = None,
hypothetical: bool = False,
active: bool = False,
homomultimer: int = 1
)
Bases: Species, CellDesignerModelElement
Base class for species
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'733f91e2-f0ed-43ee-8a62-a4f9398c5225'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
compartment
|
Compartment | None
|
|
None
|
hypothetical
|
bool
|
Whether the species is hypothetical or not |
False
|
active
|
bool
|
Whether the species is active or not |
False
|
homomultimer
|
int
|
The number of subunits forming the species |
1
|
SpeciesTemplate
dataclass
SpeciesTemplate(
*, id_: str = get_uuid4_as_str(), name: str
)
Bases: CellDesignerModelElement
Base class for species templates
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'7626ea42-1e04-45b1-ab2d-cc154e638c22'
|
name
|
str
|
The name of the species template |
required |
StateTransition
dataclass
StateTransition(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
reversible: bool,
compartment: Compartment | None = None,
reactants: frozenset[Reactant] = frozenset(),
products: frozenset[Product] = frozenset(),
modifiers: frozenset[
Modulator | UnknownModulator
] = frozenset()
)
Bases: Reaction
Class for state transitions
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'010ae057-dc5d-4712-bfcb-5ae2db649f79'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
reversible
|
bool
|
|
required |
compartment
|
Compartment | None
|
|
None
|
StateTransitionLayout
dataclass
StateTransitionLayout(
*,
_left_connector_fraction: float = 0.4,
_right_connector_fraction: float = 0.6,
reaction_node_height: float = 10.0,
reaction_node_width: float = 10.0,
reaction_node_segment: int = 1,
reaction_node_stroke: (
NoneValueType | Color | None
) = black,
reaction_node_stroke_width: float | None = 1.0,
reaction_node_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
reaction_node_stroke_dashoffset: float | None = None,
reaction_node_fill: (
NoneValueType | Color | None
) = white,
reaction_node_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
reaction_node_filter: (
NoneValueType | Filter | None
) = None,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 2.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 2.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_arrowhead_fill: (
NoneValueType | Color | None
) = black,
end_arrowhead_filter: (
NoneValueType | Filter | None
) = None,
end_arrowhead_stroke: (
NoneValueType | Color | None
) = black,
end_arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
end_arrowhead_stroke_dashoffset: float | None = None,
end_arrowhead_stroke_width: float | None = 1.0,
end_arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
start_arrowhead_fill: (
NoneValueType | Color | None
) = black,
start_arrowhead_filter: (
NoneValueType | Filter | None
) = None,
start_arrowhead_stroke: (
NoneValueType | Color | None
) = black,
start_arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
start_arrowhead_stroke_dashoffset: float | None = None,
start_arrowhead_stroke_width: float | None = 1.0,
start_arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
reversible: bool = False,
end_arrowhead_height: float = 8.0,
end_arrowhead_width: float = 15.0,
start_arrowhead_height: float = 8.0,
start_arrowhead_width: float = 15.0
)
Bases: _ReactionLayout, _ReactionNodeMixin
Class for state transition layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
_left_connector_fraction
|
float
|
|
0.4
|
_right_connector_fraction
|
float
|
|
0.6
|
reaction_node_height
|
float
|
|
10.0
|
reaction_node_width
|
float
|
|
10.0
|
reaction_node_segment
|
int
|
|
1
|
reaction_node_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
reaction_node_stroke_width
|
float | None
|
|
1.0
|
reaction_node_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
reaction_node_stroke_dashoffset
|
float | None
|
|
None
|
reaction_node_fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
reaction_node_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
reaction_node_filter
|
NoneValueType | Filter | None
|
|
None
|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'63313fb8-91e2-44b5-850f-086305734c28'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
|
2.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The path stroke dasharray of the arc |
None
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
|
2.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
end_arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
end_arrowhead_filter
|
NoneValueType | Filter | None
|
|
None
|
end_arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
end_arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
end_arrowhead_stroke_dashoffset
|
float | None
|
|
None
|
end_arrowhead_stroke_width
|
float | None
|
|
1.0
|
end_arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
start_arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
start_arrowhead_filter
|
NoneValueType | Filter | None
|
|
None
|
start_arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
start_arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
start_arrowhead_stroke_dashoffset
|
float | None
|
|
None
|
start_arrowhead_stroke_width
|
float | None
|
|
1.0
|
start_arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
reversible
|
bool
|
|
False
|
end_arrowhead_height
|
float
|
|
8.0
|
end_arrowhead_width
|
float
|
|
15.0
|
start_arrowhead_height
|
float
|
|
8.0
|
start_arrowhead_width
|
float
|
|
15.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_arrowhead_base |
Return the base anchor point of the double-headed arc end arrowhead |
end_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
end_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. |
end_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc end arrowhead |
end_arrowhead_length |
Return the length of the double-headed arc end arrowhead |
end_arrowhead_tip |
Return the tip anchor point of the double-headed arc end arrowhead |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the double-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_arrowhead_base |
Return the base anchor point of the double-headed arc start arrowhead |
start_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
start_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. |
start_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc start arrowhead |
start_arrowhead_length |
Return the length of the double-headed arc start arrowhead |
start_arrowhead_tip |
Return the tip anchor point of the double-headed arc start arrowhead |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_arrowhead_base
end_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 | |
end_arrowhead_bbox
end_arrowhead_bbox()
Return the bounding box of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1400 1401 1402 1403 1404 | |
end_arrowhead_border
end_arrowhead_border(point)
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 | |
end_arrowhead_drawing_elements
end_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 | |
end_arrowhead_length
end_arrowhead_length() -> float
Return the length of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1370 1371 1372 1373 1374 1375 1376 1377 | |
end_arrowhead_tip
end_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1379 1380 1381 1382 1383 1384 1385 1386 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the double-headed arc path
Source code in src/momapy/core.py
1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
Source code in src/momapy/celldesigner/core.py
793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_arrowhead_base
start_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 | |
start_arrowhead_bbox
start_arrowhead_bbox() -> Bbox
Return the bounding box of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1353 1354 1355 1356 1357 | |
start_arrowhead_border
start_arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 | |
start_arrowhead_drawing_elements
start_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 | |
start_arrowhead_length
start_arrowhead_length() -> float
Return the length of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1321 1322 1323 1324 1325 1326 1327 1328 | |
start_arrowhead_tip
start_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1330 1331 1332 1333 1334 1335 1336 1337 1338 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
StructuralState
dataclass
StructuralState(
*,
id_: str = get_uuid4_as_str(),
value: str | None = None
)
Bases: CellDesignerModelElement
Class for structural states
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'a19b11d2-45e5-4bc6-b39a-191d420f6f33'
|
value
|
str | None
|
The value of the structural state |
None
|
StructuralStateLayout
dataclass
StructuralStateLayout(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float = 16.0,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 50.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None
)
Bases: _SimpleNodeMixin, CellDesignerNode
Class for structural states layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'ccfb14b8-9758-49ec-9560-d7b2bae803ec'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
16.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
50.0
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
label_center |
Return the label center anchor of the node |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
830 831 832 833 834 835 836 837 838 839 840 841 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/core.py
719 720 721 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
711 712 713 714 715 716 717 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
723 724 725 726 727 728 729 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
label_center
label_center() -> Point
Return the label center anchor of the node
Source code in src/momapy/core.py
791 792 793 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/core.py
691 692 693 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
703 704 705 706 707 708 709 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
695 696 697 698 699 700 701 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
683 684 685 686 687 688 689 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
675 676 677 678 679 680 681 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/core.py
747 748 749 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
731 732 733 734 735 736 737 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
739 740 741 742 743 744 745 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
751 752 753 754 755 756 757 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
759 760 761 762 763 764 765 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/core.py
775 776 777 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
779 780 781 782 783 784 785 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
767 768 769 770 771 772 773 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
Transcription
dataclass
Transcription(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
reversible: bool,
compartment: Compartment | None = None,
reactants: frozenset[Reactant] = frozenset(),
products: frozenset[Product] = frozenset(),
modifiers: frozenset[
Modulator | UnknownModulator
] = frozenset()
)
Bases: Reaction
Class for transcriptions
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'9508c81a-a18e-4aef-ab83-6ded5a8732df'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
reversible
|
bool
|
|
required |
compartment
|
Compartment | None
|
|
None
|
TranscriptionLayout
dataclass
TranscriptionLayout(
*,
_left_connector_fraction: float = 0.4,
_right_connector_fraction: float = 0.6,
reaction_node_height: float = 10.0,
reaction_node_width: float = 10.0,
reaction_node_segment: int = 1,
reaction_node_stroke: (
NoneValueType | Color | None
) = black,
reaction_node_stroke_width: float | None = 1.0,
reaction_node_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
reaction_node_stroke_dashoffset: float | None = None,
reaction_node_fill: (
NoneValueType | Color | None
) = white,
reaction_node_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
reaction_node_filter: (
NoneValueType | Filter | None
) = None,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 2.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (12, 4, 2, 4, 2, 4),
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 2.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_arrowhead_fill: (
NoneValueType | Color | None
) = black,
end_arrowhead_filter: (
NoneValueType | Filter | None
) = None,
end_arrowhead_stroke: (
NoneValueType | Color | None
) = black,
end_arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
end_arrowhead_stroke_dashoffset: float | None = None,
end_arrowhead_stroke_width: float | None = 1.0,
end_arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
start_arrowhead_fill: (
NoneValueType | Color | None
) = black,
start_arrowhead_filter: (
NoneValueType | Filter | None
) = None,
start_arrowhead_stroke: (
NoneValueType | Color | None
) = black,
start_arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
start_arrowhead_stroke_dashoffset: float | None = None,
start_arrowhead_stroke_width: float | None = 1.0,
start_arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
reversible: bool = False,
end_arrowhead_height: float = 8.0,
end_arrowhead_width: float = 15.0,
start_arrowhead_height: float = 8.0,
start_arrowhead_width: float = 15.0
)
Bases: _ReactionLayout, _ReactionNodeMixin
Class for transcription layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
_left_connector_fraction
|
float
|
|
0.4
|
_right_connector_fraction
|
float
|
|
0.6
|
reaction_node_height
|
float
|
|
10.0
|
reaction_node_width
|
float
|
|
10.0
|
reaction_node_segment
|
int
|
|
1
|
reaction_node_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
reaction_node_stroke_width
|
float | None
|
|
1.0
|
reaction_node_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
reaction_node_stroke_dashoffset
|
float | None
|
|
None
|
reaction_node_fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
reaction_node_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
reaction_node_filter
|
NoneValueType | Filter | None
|
|
None
|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'94248254-85ca-4986-b3b5-c1b8c31c9095'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
|
2.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(12, 4, 2, 4, 2, 4)
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
|
2.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
end_arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
end_arrowhead_filter
|
NoneValueType | Filter | None
|
|
None
|
end_arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
end_arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
end_arrowhead_stroke_dashoffset
|
float | None
|
|
None
|
end_arrowhead_stroke_width
|
float | None
|
|
1.0
|
end_arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
start_arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
start_arrowhead_filter
|
NoneValueType | Filter | None
|
|
None
|
start_arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
start_arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
start_arrowhead_stroke_dashoffset
|
float | None
|
|
None
|
start_arrowhead_stroke_width
|
float | None
|
|
1.0
|
start_arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
reversible
|
bool
|
|
False
|
end_arrowhead_height
|
float
|
|
8.0
|
end_arrowhead_width
|
float
|
|
15.0
|
start_arrowhead_height
|
float
|
|
8.0
|
start_arrowhead_width
|
float
|
|
15.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_arrowhead_base |
Return the base anchor point of the double-headed arc end arrowhead |
end_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
end_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. |
end_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc end arrowhead |
end_arrowhead_length |
Return the length of the double-headed arc end arrowhead |
end_arrowhead_tip |
Return the tip anchor point of the double-headed arc end arrowhead |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the double-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_arrowhead_base |
Return the base anchor point of the double-headed arc start arrowhead |
start_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
start_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. |
start_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc start arrowhead |
start_arrowhead_length |
Return the length of the double-headed arc start arrowhead |
start_arrowhead_tip |
Return the tip anchor point of the double-headed arc start arrowhead |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_arrowhead_base
end_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 | |
end_arrowhead_bbox
end_arrowhead_bbox()
Return the bounding box of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1400 1401 1402 1403 1404 | |
end_arrowhead_border
end_arrowhead_border(point)
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 | |
end_arrowhead_drawing_elements
end_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 | |
end_arrowhead_length
end_arrowhead_length() -> float
Return the length of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1370 1371 1372 1373 1374 1375 1376 1377 | |
end_arrowhead_tip
end_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1379 1380 1381 1382 1383 1384 1385 1386 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the double-headed arc path
Source code in src/momapy/core.py
1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
Source code in src/momapy/celldesigner/core.py
793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_arrowhead_base
start_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 | |
start_arrowhead_bbox
start_arrowhead_bbox() -> Bbox
Return the bounding box of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1353 1354 1355 1356 1357 | |
start_arrowhead_border
start_arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 | |
start_arrowhead_drawing_elements
start_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 | |
start_arrowhead_length
start_arrowhead_length() -> float
Return the length of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1321 1322 1323 1324 1325 1326 1327 1328 | |
start_arrowhead_tip
start_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1330 1331 1332 1333 1334 1335 1336 1337 1338 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
TranscriptionStartingSiteL
dataclass
TranscriptionStartingSiteL(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
active: bool = False
)
Bases: Region
Class for left transcription starting sites
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'df506c3e-ee0c-4ebe-a555-44d2bb76da3b'
|
name
|
str | None
|
The name of the region |
None
|
active
|
bool
|
Whether the region is active or not |
False
|
TranscriptionStartingSiteR
dataclass
TranscriptionStartingSiteR(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
active: bool = False
)
Bases: Region
Class for right transcription starting sites
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'48970f4b-2dbd-4013-8630-ebda04c02801'
|
name
|
str | None
|
The name of the region |
None
|
active
|
bool
|
Whether the region is active or not |
False
|
Translation
dataclass
Translation(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
reversible: bool,
compartment: Compartment | None = None,
reactants: frozenset[Reactant] = frozenset(),
products: frozenset[Product] = frozenset(),
modifiers: frozenset[
Modulator | UnknownModulator
] = frozenset()
)
Bases: Reaction
Class for translation
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'0084f158-f3b4-4cff-ab30-9ab2d1fa0082'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
reversible
|
bool
|
|
required |
compartment
|
Compartment | None
|
|
None
|
TranslationLayout
dataclass
TranslationLayout(
*,
_left_connector_fraction: float = 0.4,
_right_connector_fraction: float = 0.6,
reaction_node_height: float = 10.0,
reaction_node_width: float = 10.0,
reaction_node_segment: int = 1,
reaction_node_stroke: (
NoneValueType | Color | None
) = black,
reaction_node_stroke_width: float | None = 1.0,
reaction_node_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
reaction_node_stroke_dashoffset: float | None = None,
reaction_node_fill: (
NoneValueType | Color | None
) = white,
reaction_node_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
reaction_node_filter: (
NoneValueType | Filter | None
) = None,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 2.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (12, 4, 2, 4),
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 2.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_arrowhead_fill: (
NoneValueType | Color | None
) = black,
end_arrowhead_filter: (
NoneValueType | Filter | None
) = None,
end_arrowhead_stroke: (
NoneValueType | Color | None
) = black,
end_arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
end_arrowhead_stroke_dashoffset: float | None = None,
end_arrowhead_stroke_width: float | None = 1.0,
end_arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
start_arrowhead_fill: (
NoneValueType | Color | None
) = black,
start_arrowhead_filter: (
NoneValueType | Filter | None
) = None,
start_arrowhead_stroke: (
NoneValueType | Color | None
) = black,
start_arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
start_arrowhead_stroke_dashoffset: float | None = None,
start_arrowhead_stroke_width: float | None = 1.0,
start_arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
reversible: bool = False,
end_arrowhead_height: float = 8.0,
end_arrowhead_width: float = 15.0,
start_arrowhead_height: float = 8.0,
start_arrowhead_width: float = 15.0
)
Bases: _ReactionLayout, _ReactionNodeMixin
Class for translation layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
_left_connector_fraction
|
float
|
|
0.4
|
_right_connector_fraction
|
float
|
|
0.6
|
reaction_node_height
|
float
|
|
10.0
|
reaction_node_width
|
float
|
|
10.0
|
reaction_node_segment
|
int
|
|
1
|
reaction_node_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
reaction_node_stroke_width
|
float | None
|
|
1.0
|
reaction_node_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
reaction_node_stroke_dashoffset
|
float | None
|
|
None
|
reaction_node_fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
reaction_node_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
reaction_node_filter
|
NoneValueType | Filter | None
|
|
None
|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'979f59d4-f273-4a71-a26b-06bac79b8986'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
|
2.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(12, 4, 2, 4)
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
|
2.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
end_arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
end_arrowhead_filter
|
NoneValueType | Filter | None
|
|
None
|
end_arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
end_arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
end_arrowhead_stroke_dashoffset
|
float | None
|
|
None
|
end_arrowhead_stroke_width
|
float | None
|
|
1.0
|
end_arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
start_arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
start_arrowhead_filter
|
NoneValueType | Filter | None
|
|
None
|
start_arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
start_arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
start_arrowhead_stroke_dashoffset
|
float | None
|
|
None
|
start_arrowhead_stroke_width
|
float | None
|
|
1.0
|
start_arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
reversible
|
bool
|
|
False
|
end_arrowhead_height
|
float
|
|
8.0
|
end_arrowhead_width
|
float
|
|
15.0
|
start_arrowhead_height
|
float
|
|
8.0
|
start_arrowhead_width
|
float
|
|
15.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_arrowhead_base |
Return the base anchor point of the double-headed arc end arrowhead |
end_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
end_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. |
end_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc end arrowhead |
end_arrowhead_length |
Return the length of the double-headed arc end arrowhead |
end_arrowhead_tip |
Return the tip anchor point of the double-headed arc end arrowhead |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the double-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_arrowhead_base |
Return the base anchor point of the double-headed arc start arrowhead |
start_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
start_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. |
start_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc start arrowhead |
start_arrowhead_length |
Return the length of the double-headed arc start arrowhead |
start_arrowhead_tip |
Return the tip anchor point of the double-headed arc start arrowhead |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_arrowhead_base
end_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 | |
end_arrowhead_bbox
end_arrowhead_bbox()
Return the bounding box of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1400 1401 1402 1403 1404 | |
end_arrowhead_border
end_arrowhead_border(point)
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 | |
end_arrowhead_drawing_elements
end_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 | |
end_arrowhead_length
end_arrowhead_length() -> float
Return the length of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1370 1371 1372 1373 1374 1375 1376 1377 | |
end_arrowhead_tip
end_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1379 1380 1381 1382 1383 1384 1385 1386 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the double-headed arc path
Source code in src/momapy/core.py
1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
Source code in src/momapy/celldesigner/core.py
793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_arrowhead_base
start_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 | |
start_arrowhead_bbox
start_arrowhead_bbox() -> Bbox
Return the bounding box of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1353 1354 1355 1356 1357 | |
start_arrowhead_border
start_arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 | |
start_arrowhead_drawing_elements
start_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 | |
start_arrowhead_length
start_arrowhead_length() -> float
Return the length of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1321 1322 1323 1324 1325 1326 1327 1328 | |
start_arrowhead_tip
start_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1330 1331 1332 1333 1334 1335 1336 1337 1338 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
Transport
dataclass
Transport(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
reversible: bool,
compartment: Compartment | None = None,
reactants: frozenset[Reactant] = frozenset(),
products: frozenset[Product] = frozenset(),
modifiers: frozenset[
Modulator | UnknownModulator
] = frozenset()
)
Bases: Reaction
Class for transports
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'316d8d46-2e89-4535-90a8-912f8fd4bb93'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
reversible
|
bool
|
|
required |
compartment
|
Compartment | None
|
|
None
|
TransportLayout
dataclass
TransportLayout(
*,
_left_connector_fraction: float = 0.4,
_right_connector_fraction: float = 0.6,
reaction_node_height: float = 10.0,
reaction_node_width: float = 10.0,
reaction_node_segment: int = 1,
reaction_node_stroke: (
NoneValueType | Color | None
) = black,
reaction_node_stroke_width: float | None = 1.0,
reaction_node_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
reaction_node_stroke_dashoffset: float | None = None,
reaction_node_fill: (
NoneValueType | Color | None
) = white,
reaction_node_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
reaction_node_filter: (
NoneValueType | Filter | None
) = None,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 2.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 2.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_arrowhead_fill: (
NoneValueType | Color | None
) = black,
end_arrowhead_filter: (
NoneValueType | Filter | None
) = None,
end_arrowhead_stroke: (
NoneValueType | Color | None
) = black,
end_arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
end_arrowhead_stroke_dashoffset: float | None = None,
end_arrowhead_stroke_width: float | None = 1.0,
end_arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
start_arrowhead_fill: (
NoneValueType | Color | None
) = black,
start_arrowhead_filter: (
NoneValueType | Filter | None
) = None,
start_arrowhead_stroke: (
NoneValueType | Color | None
) = black,
start_arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
start_arrowhead_stroke_dashoffset: float | None = None,
start_arrowhead_stroke_width: float | None = 1.0,
start_arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
reversible: bool = False,
end_arrowhead_bar_height: float = 8.0,
end_arrowhead_sep: float = 5.0,
end_arrowhead_triangle_height: float = 8.0,
end_arrowhead_triangle_width: float = 15.0,
start_arrowhead_bar_height: float = 8.0,
start_arrowhead_sep: float = 4.0,
start_arrowhead_triangle_height: float = 8.0,
start_arrowhead_triangle_width: float = 15.0
)
Bases: _ReactionLayout, _ReactionNodeMixin
Class for transport layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
_left_connector_fraction
|
float
|
|
0.4
|
_right_connector_fraction
|
float
|
|
0.6
|
reaction_node_height
|
float
|
|
10.0
|
reaction_node_width
|
float
|
|
10.0
|
reaction_node_segment
|
int
|
|
1
|
reaction_node_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
reaction_node_stroke_width
|
float | None
|
|
1.0
|
reaction_node_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
reaction_node_stroke_dashoffset
|
float | None
|
|
None
|
reaction_node_fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
reaction_node_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
reaction_node_filter
|
NoneValueType | Filter | None
|
|
None
|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'b8b1eb3c-8a40-4b3f-8dbc-b6931c297631'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
|
2.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The path stroke dasharray of the arc |
None
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
|
2.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
end_arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
end_arrowhead_filter
|
NoneValueType | Filter | None
|
|
None
|
end_arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
end_arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
end_arrowhead_stroke_dashoffset
|
float | None
|
|
None
|
end_arrowhead_stroke_width
|
float | None
|
|
1.0
|
end_arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
start_arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
start_arrowhead_filter
|
NoneValueType | Filter | None
|
|
None
|
start_arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
start_arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
start_arrowhead_stroke_dashoffset
|
float | None
|
|
None
|
start_arrowhead_stroke_width
|
float | None
|
|
1.0
|
start_arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
reversible
|
bool
|
|
False
|
end_arrowhead_bar_height
|
float
|
|
8.0
|
end_arrowhead_sep
|
float
|
|
5.0
|
end_arrowhead_triangle_height
|
float
|
|
8.0
|
end_arrowhead_triangle_width
|
float
|
|
15.0
|
start_arrowhead_bar_height
|
float
|
|
8.0
|
start_arrowhead_sep
|
float
|
|
4.0
|
start_arrowhead_triangle_height
|
float
|
|
8.0
|
start_arrowhead_triangle_width
|
float
|
|
15.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_arrowhead_base |
Return the base anchor point of the double-headed arc end arrowhead |
end_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
end_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. |
end_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc end arrowhead |
end_arrowhead_length |
Return the length of the double-headed arc end arrowhead |
end_arrowhead_tip |
Return the tip anchor point of the double-headed arc end arrowhead |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the double-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_arrowhead_base |
Return the base anchor point of the double-headed arc start arrowhead |
start_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
start_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. |
start_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc start arrowhead |
start_arrowhead_length |
Return the length of the double-headed arc start arrowhead |
start_arrowhead_tip |
Return the tip anchor point of the double-headed arc start arrowhead |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_arrowhead_base
end_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 | |
end_arrowhead_bbox
end_arrowhead_bbox()
Return the bounding box of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1400 1401 1402 1403 1404 | |
end_arrowhead_border
end_arrowhead_border(point)
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 | |
end_arrowhead_drawing_elements
end_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 | |
end_arrowhead_length
end_arrowhead_length() -> float
Return the length of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1370 1371 1372 1373 1374 1375 1376 1377 | |
end_arrowhead_tip
end_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1379 1380 1381 1382 1383 1384 1385 1386 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the double-headed arc path
Source code in src/momapy/core.py
1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
Source code in src/momapy/celldesigner/core.py
793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_arrowhead_base
start_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 | |
start_arrowhead_bbox
start_arrowhead_bbox() -> Bbox
Return the bounding box of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1353 1354 1355 1356 1357 | |
start_arrowhead_border
start_arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 | |
start_arrowhead_drawing_elements
start_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 | |
start_arrowhead_length
start_arrowhead_length() -> float
Return the length of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1321 1322 1323 1324 1325 1326 1327 1328 | |
start_arrowhead_tip
start_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1330 1331 1332 1333 1334 1335 1336 1337 1338 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
Trigger
dataclass
Trigger(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
referred_species: Species | BooleanLogicGate
)
Bases: Modulator
Class for triggers
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'21e529c5-1215-4b87-826a-d9ff2b7f624f'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
referred_species
|
Species | BooleanLogicGate
|
The species the modifier refers to |
required |
Triggering
dataclass
Triggering(
*,
id_: str = get_uuid4_as_str(),
source: Species | BooleanLogicGate,
target: Species | None
)
Bases: Modulation
Class for triggerings
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'8f0cc64f-22de-4c66-848f-bdfa5ac4ea98'
|
source
|
Species | BooleanLogicGate
|
The source of the influence |
required |
target
|
Species | None
|
The target of the influence |
required |
TriggeringLayout
dataclass
TriggeringLayout(
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 0.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 0.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_fill: NoneValueType | Color | None = white,
arrowhead_filter: NoneValueType | Filter | None = None,
arrowhead_stroke: NoneValueType | Color | None = black,
arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
arrowhead_stroke_dashoffset: float | None = None,
arrowhead_stroke_width: float | None = 1.0,
arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_bar_height: float = 8.0,
arrowhead_sep: float = 5.0,
arrowhead_triangle_height: float = 10.0,
arrowhead_triangle_width: float = 15.0
)
Bases: CellDesignerSingleHeadedArc
Class for triggering layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'd6f198b5-5f13-4b3b-902a-908eba7e3a3b'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
The length the end of the arc will be shorten by |
0.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The path stroke dasharray of the arc |
None
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
The length the start of the arc will be shorten by |
0.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
arrowhead_filter
|
NoneValueType | Filter | None
|
The arrowhead filter of the arc |
None
|
arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The arrowhead stroke dasharray of the arc |
None
|
arrowhead_stroke_dashoffset
|
float | None
|
The arrowhead stroke dashoffset of the arc |
None
|
arrowhead_stroke_width
|
float | None
|
|
1.0
|
arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
The arrowhead transform of the arc |
None
|
arrowhead_bar_height
|
float
|
|
8.0
|
arrowhead_sep
|
float
|
|
5.0
|
arrowhead_triangle_height
|
float
|
|
10.0
|
arrowhead_triangle_width
|
float
|
|
15.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
1089 1090 1091 1092 1093 1094 1095 1096 1097 | |
arrowhead_bbox
arrowhead_bbox() -> Bbox
Return the bounding box of the single-headed arc arrowhead
Source code in src/momapy/core.py
1099 1100 1101 1102 1103 | |
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 | |
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 | |
arrowhead_length
arrowhead_length() -> float
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
1071 1072 1073 1074 1075 1076 1077 1078 | |
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
1080 1081 1082 1083 1084 1085 1086 1087 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
TruncatedProtein
dataclass
TruncatedProtein(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
compartment: Compartment | None = None,
hypothetical: bool = False,
active: bool = False,
homomultimer: int = 1,
template: TruncatedProteinTemplate,
modifications: frozenset[Modification] = frozenset(),
structural_states: frozenset[
StructuralState
] = frozenset()
)
Bases: Protein
Class for truncated proteins
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'd904e94a-0294-4d6f-a78f-9e7fc8d314dd'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
compartment
|
Compartment | None
|
|
None
|
hypothetical
|
bool
|
Whether the species is hypothetical or not |
False
|
active
|
bool
|
Whether the species is active or not |
False
|
homomultimer
|
int
|
The number of subunits forming the species |
1
|
template
|
TruncatedProteinTemplate
|
The template of the truncated protein |
required |
TruncatedProteinLayout
dataclass
TruncatedProteinLayout(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
offset: float = 3.0,
subunits_stroke: (
tuple[NoneValueType | Color] | None
) = None,
subunits_stroke_width: (
tuple[NoneValueType | float] | None
) = None,
subunits_stroke_dasharray: (
tuple[NoneValueType | tuple[float]] | None
) = None,
subunits_stroke_dashoffset: tuple[float] | None = None,
subunits_fill: (
tuple[NoneValueType | Color] | None
) = None,
subunits_transform: (
tuple[NoneValueType | tuple[Transformation]] | None
) = None,
subunits_filter: (
tuple[NoneValueType | Filter] | None
) = None,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float = 30.0,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 60.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
n: int = 1,
rounded_corners: float = 15.0,
vertical_truncation: float = 0.4,
horizontal_truncation: float = 0.2
)
Bases: _MultiNodeMixin, CellDesignerNode
Class for truncated protein layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'c683ab00-fd6f-4cb9-8f91-cf9d31a66f5b'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
30.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
60.0
|
offset
|
float
|
|
3.0
|
subunits_stroke
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_stroke_width
|
tuple[Union[NoneValueType, float]] | None
|
|
None
|
subunits_stroke_dasharray
|
tuple[Union[NoneValueType, tuple[float]]] | None
|
|
None
|
subunits_stroke_dashoffset
|
tuple[float] | None
|
|
None
|
subunits_fill
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_transform
|
tuple[Union[NoneValueType, tuple[Transformation]]] | None
|
|
None
|
subunits_filter
|
tuple[Union[NoneValueType, Filter]] | None
|
|
None
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
n
|
int
|
|
1
|
rounded_corners
|
float
|
|
15.0
|
vertical_truncation
|
float
|
|
0.4
|
horizontal_truncation
|
float
|
|
0.2
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
830 831 832 833 834 835 836 837 838 839 840 841 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/core.py
719 720 721 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
711 712 713 714 715 716 717 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
723 724 725 726 727 728 729 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/core.py
691 692 693 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
703 704 705 706 707 708 709 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
695 696 697 698 699 700 701 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
683 684 685 686 687 688 689 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
675 676 677 678 679 680 681 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/core.py
747 748 749 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
731 732 733 734 735 736 737 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
739 740 741 742 743 744 745 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
751 752 753 754 755 756 757 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
759 760 761 762 763 764 765 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/core.py
775 776 777 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
779 780 781 782 783 784 785 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
767 768 769 770 771 772 773 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
TruncatedProteinTemplate
dataclass
TruncatedProteinTemplate(
*,
id_: str = get_uuid4_as_str(),
name: str,
modification_residues: frozenset[
ModificationResidue
] = frozenset()
)
Bases: ProteinTemplate
Class for truncated protein templates
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'ea3c175d-bad8-4d0c-9098-b6d351de39e2'
|
name
|
str
|
The name of the species template |
required |
Truncation
dataclass
Truncation(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
reversible: bool,
compartment: Compartment | None = None,
reactants: frozenset[Reactant] = frozenset(),
products: frozenset[Product] = frozenset(),
modifiers: frozenset[
Modulator | UnknownModulator
] = frozenset()
)
Bases: Reaction
Class for truncations
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'c611d01b-c8d0-46f6-8edc-2c02efd7d4b2'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
reversible
|
bool
|
|
required |
compartment
|
Compartment | None
|
|
None
|
TruncationLayout
dataclass
TruncationLayout(
*,
_left_connector_fraction: float = 0.4,
_right_connector_fraction: float = 0.6,
reaction_node_height: float = 10.0,
reaction_node_width: float = 10.0,
reaction_node_segment: int = 1,
reaction_node_stroke: (
NoneValueType | Color | None
) = black,
reaction_node_stroke_width: float | None = 1.0,
reaction_node_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
reaction_node_stroke_dashoffset: float | None = None,
reaction_node_fill: (
NoneValueType | Color | None
) = white,
reaction_node_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
reaction_node_filter: (
NoneValueType | Filter | None
) = None,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 2.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 2.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_arrowhead_fill: (
NoneValueType | Color | None
) = white,
end_arrowhead_filter: (
NoneValueType | Filter | None
) = None,
end_arrowhead_stroke: (
NoneValueType | Color | None
) = black,
end_arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
end_arrowhead_stroke_dashoffset: float | None = None,
end_arrowhead_stroke_width: float | None = 1.0,
end_arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
start_arrowhead_fill: (
NoneValueType | Color | None
) = black,
start_arrowhead_filter: (
NoneValueType | Filter | None
) = None,
start_arrowhead_stroke: (
NoneValueType | Color | None
) = black,
start_arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
start_arrowhead_stroke_dashoffset: float | None = None,
start_arrowhead_stroke_width: float | None = 1.0,
start_arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
reversible: bool = False,
end_arrowhead_height: float = 10.0,
end_arrowhead_sep: float = 2.0,
end_arrowhead_width: float = 10.0,
start_arrowhead_height: float = 8.0,
start_arrowhead_width: float = 15.0
)
Bases: _ReactionLayout, _ReactionNodeMixin
Class for truncation layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
_left_connector_fraction
|
float
|
|
0.4
|
_right_connector_fraction
|
float
|
|
0.6
|
reaction_node_height
|
float
|
|
10.0
|
reaction_node_width
|
float
|
|
10.0
|
reaction_node_segment
|
int
|
|
1
|
reaction_node_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
reaction_node_stroke_width
|
float | None
|
|
1.0
|
reaction_node_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
reaction_node_stroke_dashoffset
|
float | None
|
|
None
|
reaction_node_fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
reaction_node_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
reaction_node_filter
|
NoneValueType | Filter | None
|
|
None
|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'9c286b5f-924f-4deb-b155-2e2e82a15828'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
|
2.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The path stroke dasharray of the arc |
None
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
|
2.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
end_arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
end_arrowhead_filter
|
NoneValueType | Filter | None
|
|
None
|
end_arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
end_arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
end_arrowhead_stroke_dashoffset
|
float | None
|
|
None
|
end_arrowhead_stroke_width
|
float | None
|
|
1.0
|
end_arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
start_arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
start_arrowhead_filter
|
NoneValueType | Filter | None
|
|
None
|
start_arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
start_arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
start_arrowhead_stroke_dashoffset
|
float | None
|
|
None
|
start_arrowhead_stroke_width
|
float | None
|
|
1.0
|
start_arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
reversible
|
bool
|
|
False
|
end_arrowhead_height
|
float
|
|
10.0
|
end_arrowhead_sep
|
float
|
|
2.0
|
end_arrowhead_width
|
float
|
|
10.0
|
start_arrowhead_height
|
float
|
|
8.0
|
start_arrowhead_width
|
float
|
|
15.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_arrowhead_base |
Return the base anchor point of the double-headed arc end arrowhead |
end_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
end_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. |
end_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc end arrowhead |
end_arrowhead_length |
Return the length of the double-headed arc end arrowhead |
end_arrowhead_tip |
Return the tip anchor point of the double-headed arc end arrowhead |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the double-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_arrowhead_base |
Return the base anchor point of the double-headed arc start arrowhead |
start_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
start_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. |
start_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc start arrowhead |
start_arrowhead_length |
Return the length of the double-headed arc start arrowhead |
start_arrowhead_tip |
Return the tip anchor point of the double-headed arc start arrowhead |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_arrowhead_base
end_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 | |
end_arrowhead_bbox
end_arrowhead_bbox()
Return the bounding box of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1400 1401 1402 1403 1404 | |
end_arrowhead_border
end_arrowhead_border(point)
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 | |
end_arrowhead_drawing_elements
end_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 | |
end_arrowhead_length
end_arrowhead_length() -> float
Return the length of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1370 1371 1372 1373 1374 1375 1376 1377 | |
end_arrowhead_tip
end_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1379 1380 1381 1382 1383 1384 1385 1386 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the double-headed arc path
Source code in src/momapy/core.py
1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
Source code in src/momapy/celldesigner/core.py
793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_arrowhead_base
start_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 | |
start_arrowhead_bbox
start_arrowhead_bbox() -> Bbox
Return the bounding box of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1353 1354 1355 1356 1357 | |
start_arrowhead_border
start_arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 | |
start_arrowhead_drawing_elements
start_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 | |
start_arrowhead_length
start_arrowhead_length() -> float
Return the length of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1321 1322 1323 1324 1325 1326 1327 1328 | |
start_arrowhead_tip
start_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1330 1331 1332 1333 1334 1335 1336 1337 1338 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
Unknown
dataclass
Unknown(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
compartment: Compartment | None = None,
hypothetical: bool = False,
active: bool = False,
homomultimer: int = 1
)
Bases: Species
Class for unknown species
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'e06f8a8c-e5d0-4ef3-b0a4-1f87f706af93'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
compartment
|
Compartment | None
|
|
None
|
hypothetical
|
bool
|
Whether the species is hypothetical or not |
False
|
active
|
bool
|
Whether the species is active or not |
False
|
homomultimer
|
int
|
The number of subunits forming the species |
1
|
UnknownCatalysis
dataclass
UnknownCatalysis(
*,
id_: str = get_uuid4_as_str(),
source: Species | BooleanLogicGate,
target: Species | None
)
Bases: UnknownModulation
Class for unknown catalyses
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'24cdd199-8bcb-4427-a5be-6bed2fde49ce'
|
source
|
Species | BooleanLogicGate
|
The source of the influence |
required |
target
|
Species | None
|
The target of the influence |
required |
UnknownCatalysisLayout
dataclass
UnknownCatalysisLayout(
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 0.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (12, 4),
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 0.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_fill: NoneValueType | Color | None = white,
arrowhead_filter: NoneValueType | Filter | None = None,
arrowhead_stroke: NoneValueType | Color | None = black,
arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
arrowhead_stroke_dashoffset: float | None = None,
arrowhead_stroke_width: float | None = 1.0,
arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_height: float = 7.0,
arrowhead_width: float = 7.0
)
Bases: CellDesignerSingleHeadedArc
Class for unknown catalysis layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'66357df5-d901-44d4-b9bb-d2df9e60c2df'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
The length the end of the arc will be shorten by |
0.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(12, 4)
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
The length the start of the arc will be shorten by |
0.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
arrowhead_filter
|
NoneValueType | Filter | None
|
The arrowhead filter of the arc |
None
|
arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The arrowhead stroke dasharray of the arc |
None
|
arrowhead_stroke_dashoffset
|
float | None
|
The arrowhead stroke dashoffset of the arc |
None
|
arrowhead_stroke_width
|
float | None
|
|
1.0
|
arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
The arrowhead transform of the arc |
None
|
arrowhead_height
|
float
|
|
7.0
|
arrowhead_width
|
float
|
|
7.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
1089 1090 1091 1092 1093 1094 1095 1096 1097 | |
arrowhead_bbox
arrowhead_bbox() -> Bbox
Return the bounding box of the single-headed arc arrowhead
Source code in src/momapy/core.py
1099 1100 1101 1102 1103 | |
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 | |
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 | |
arrowhead_length
arrowhead_length() -> float
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
1071 1072 1073 1074 1075 1076 1077 1078 | |
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
1080 1081 1082 1083 1084 1085 1086 1087 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
UnknownCatalyzer
dataclass
UnknownCatalyzer(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
referred_species: Species | BooleanLogicGate
)
Bases: UnknownModulator
Class for unknown catalyzers
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'221e3c12-08cc-44b0-813e-3d752b1c9970'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
referred_species
|
Species | BooleanLogicGate
|
The species the modifier refers to |
required |
UnknownGate
dataclass
UnknownGate(
*,
id_: str = get_uuid4_as_str(),
inputs: frozenset[Species] = frozenset()
)
Bases: BooleanLogicGate
Class for unknown gates
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'f739907e-1067-40f7-a36a-ff9c061939f2'
|
UnknownGateLayout
dataclass
UnknownGateLayout(
fill: NoneValueType | Color | None = white,
stroke: NoneValueType | Color | None = black,
stroke_width: float | None = 1.25,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
filter: NoneValueType | Filter | None = None,
height: float = 15.0,
label: TextLayout | None = None,
position: Point,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 15.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None
)
Bases: _SimpleNodeMixin, _TextMixin, CellDesignerNode
Class for unknown gate layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'99c85a77-5afa-4604-bbf7-b27f8639b18b'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
15.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
15.0
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
label_center |
Return the label center anchor of the node |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
830 831 832 833 834 835 836 837 838 839 840 841 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/core.py
719 720 721 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
711 712 713 714 715 716 717 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
723 724 725 726 727 728 729 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
label_center
label_center() -> Point
Return the label center anchor of the node
Source code in src/momapy/core.py
791 792 793 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/core.py
691 692 693 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
703 704 705 706 707 708 709 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
695 696 697 698 699 700 701 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
683 684 685 686 687 688 689 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
675 676 677 678 679 680 681 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/core.py
747 748 749 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
731 732 733 734 735 736 737 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
739 740 741 742 743 744 745 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
751 752 753 754 755 756 757 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
759 760 761 762 763 764 765 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/core.py
775 776 777 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
779 780 781 782 783 784 785 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
767 768 769 770 771 772 773 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
UnknownInhibition
dataclass
UnknownInhibition(
*,
id_: str = get_uuid4_as_str(),
source: Species | BooleanLogicGate,
target: Species | None
)
Bases: UnknownModulation
Class for unknown inhibitions
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'f0ee1a3b-6d9e-40c5-8a20-d62189e23a08'
|
source
|
Species | BooleanLogicGate
|
The source of the influence |
required |
target
|
Species | None
|
The target of the influence |
required |
UnknownInhibitionLayout
dataclass
UnknownInhibitionLayout(
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 3.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (12, 4),
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 0.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_fill: NoneValueType | Color | None = None,
arrowhead_filter: NoneValueType | Filter | None = None,
arrowhead_stroke: NoneValueType | Color | None = black,
arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
arrowhead_stroke_dashoffset: float | None = None,
arrowhead_stroke_width: float | None = 1.0,
arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_height: float = 10.0
)
Bases: CellDesignerSingleHeadedArc
Class for unknown inhibition layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'af25eeb2-710d-42a3-b5ba-7fb700e4b1a0'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
|
3.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(12, 4)
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
The length the start of the arc will be shorten by |
0.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
arrowhead_fill
|
NoneValueType | Color | None
|
The arrowhead fill color of the arc |
None
|
arrowhead_filter
|
NoneValueType | Filter | None
|
The arrowhead filter of the arc |
None
|
arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The arrowhead stroke dasharray of the arc |
None
|
arrowhead_stroke_dashoffset
|
float | None
|
The arrowhead stroke dashoffset of the arc |
None
|
arrowhead_stroke_width
|
float | None
|
|
1.0
|
arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
The arrowhead transform of the arc |
None
|
arrowhead_height
|
float
|
|
10.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
1089 1090 1091 1092 1093 1094 1095 1096 1097 | |
arrowhead_bbox
arrowhead_bbox() -> Bbox
Return the bounding box of the single-headed arc arrowhead
Source code in src/momapy/core.py
1099 1100 1101 1102 1103 | |
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 | |
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 | |
arrowhead_length
arrowhead_length() -> float
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
1071 1072 1073 1074 1075 1076 1077 1078 | |
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
1080 1081 1082 1083 1084 1085 1086 1087 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
UnknownInhibitor
dataclass
UnknownInhibitor(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
referred_species: Species | BooleanLogicGate
)
Bases: UnknownModulator
Class for unknown inhibitors
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'184664a4-4fcd-47b0-9aa3-8606ea8f9259'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
referred_species
|
Species | BooleanLogicGate
|
The species the modifier refers to |
required |
UnknownLayout
dataclass
UnknownLayout(
stroke_width: float | None = 1.25,
offset: float = 3.0,
subunits_stroke: (
tuple[NoneValueType | Color] | None
) = None,
subunits_stroke_width: (
tuple[NoneValueType | float] | None
) = None,
subunits_stroke_dasharray: (
tuple[NoneValueType | tuple[float]] | None
) = None,
subunits_stroke_dashoffset: tuple[float] | None = None,
subunits_fill: (
tuple[NoneValueType | Color] | None
) = None,
subunits_transform: (
tuple[NoneValueType | tuple[Transformation]] | None
) = None,
subunits_filter: (
tuple[NoneValueType | Filter] | None
) = None,
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
fill: NoneValueType | Color | None = gray,
filter: NoneValueType | Filter | None = None,
height: float = 30.0,
label: TextLayout | None = None,
position: Point,
stroke: NoneValueType | Color | None = NoneValue,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
width: float = 60.0,
active: bool = False,
active_fill: NoneValueType | Color | None = NoneValue,
active_filter: NoneValueType | Filter | None = None,
active_sep: float = 4.0,
active_stroke: NoneValueType | Color | None = black,
active_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (4, 2),
active_stroke_dashoffset: float | None = None,
active_stroke_width: float | None = 1.0,
active_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
n: int = 1
)
Bases: _MultiNodeMixin, CellDesignerNode
Class for unknown species layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'd8610650-6895-4657-82a4-76d234562706'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
fill
|
NoneValueType | Color | None
|
|
Color(red=128, green=128, blue=128, alpha=1.0)
|
filter
|
NoneValueType | Filter | None
|
The filter of the node |
None
|
height
|
float
|
|
30.0
|
label
|
TextLayout | None
|
The label of the node |
None
|
position
|
Point
|
The position of the node |
required |
stroke
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the node |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the node |
None
|
stroke_width
|
float | None
|
|
1.25
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the node |
None
|
width
|
float
|
|
60.0
|
offset
|
float
|
|
3.0
|
subunits_stroke
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_stroke_width
|
tuple[Union[NoneValueType, float]] | None
|
|
None
|
subunits_stroke_dasharray
|
tuple[Union[NoneValueType, tuple[float]]] | None
|
|
None
|
subunits_stroke_dashoffset
|
tuple[float] | None
|
|
None
|
subunits_fill
|
tuple[Union[NoneValueType, Color]] | None
|
|
None
|
subunits_transform
|
tuple[Union[NoneValueType, tuple[Transformation]]] | None
|
|
None
|
subunits_filter
|
tuple[Union[NoneValueType, Filter]] | None
|
|
None
|
active
|
bool
|
|
False
|
active_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
active_filter
|
NoneValueType | Filter | None
|
|
None
|
active_sep
|
float
|
|
4.0
|
active_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
active_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(4, 2)
|
active_stroke_dashoffset
|
float | None
|
|
None
|
active_stroke_width
|
float | None
|
|
1.0
|
active_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
n
|
int
|
|
1
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the self drawing elements of the node |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
angle
angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
830 831 832 833 834 835 836 837 838 839 840 841 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
807 808 809 810 811 812 813 814 815 | |
center
center() -> Point
Return the center anchor of the node
Source code in src/momapy/core.py
787 788 789 | |
childless
childless() -> Self
Return a copy of the node with no children
Source code in src/momapy/core.py
843 844 845 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/core.py
719 720 721 | |
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
711 712 713 714 715 716 717 | |
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
723 724 725 726 727 728 729 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/core.py
691 692 693 | |
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
703 704 705 706 707 708 709 | |
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
695 696 697 698 699 700 701 | |
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
683 684 685 686 687 688 689 | |
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
675 676 677 678 679 680 681 | |
self_angle
self_angle(
angle: float,
unit: Literal["degrees", "radians"] = "degrees",
) -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
817 818 819 820 821 822 823 824 825 826 827 828 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
795 796 797 798 799 800 801 802 803 804 805 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
Source code in src/momapy/core.py
665 666 667 668 669 | |
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the self drawing elements of the node
Source code in src/momapy/core.py
648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
size
size() -> tuple[float, float]
Return the size of the node
Source code in src/momapy/core.py
671 672 673 | |
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/core.py
747 748 749 | |
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
731 732 733 734 735 736 737 | |
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
739 740 741 742 743 744 745 | |
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
751 752 753 754 755 756 757 | |
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
759 760 761 762 763 764 765 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/core.py
775 776 777 | |
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
779 780 781 782 783 784 785 | |
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
767 768 769 770 771 772 773 | |
x
property
x: float
Return the x coordinate of the node
y
property
y: float
Return the y coordinate of the node
UnknownModulation
dataclass
UnknownModulation(
*,
id_: str = get_uuid4_as_str(),
source: Species | BooleanLogicGate,
target: Species | None
)
Bases: _Influence
Class for unknown modulations
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'ffa74101-8fc3-4300-a793-f9bf2470b254'
|
source
|
Species | BooleanLogicGate
|
The source of the influence |
required |
target
|
Species | None
|
The target of the influence |
required |
UnknownModulationLayout
dataclass
UnknownModulationLayout(
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 0.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (12, 4),
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 0.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_fill: NoneValueType | Color | None = white,
arrowhead_filter: NoneValueType | Filter | None = None,
arrowhead_stroke: NoneValueType | Color | None = black,
arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
arrowhead_stroke_dashoffset: float | None = None,
arrowhead_stroke_width: float | None = 1.0,
arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_height: float = 8.0,
arrowhead_width: float = 15.0
)
Bases: CellDesignerSingleHeadedArc
Class for unknown modulation layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'20eb3360-7b29-461f-b274-ebd9c6006d57'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
The length the end of the arc will be shorten by |
0.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(12, 4)
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
The length the start of the arc will be shorten by |
0.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
arrowhead_filter
|
NoneValueType | Filter | None
|
The arrowhead filter of the arc |
None
|
arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The arrowhead stroke dasharray of the arc |
None
|
arrowhead_stroke_dashoffset
|
float | None
|
The arrowhead stroke dashoffset of the arc |
None
|
arrowhead_stroke_width
|
float | None
|
|
1.0
|
arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
The arrowhead transform of the arc |
None
|
arrowhead_height
|
float
|
|
8.0
|
arrowhead_width
|
float
|
|
15.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
1089 1090 1091 1092 1093 1094 1095 1096 1097 | |
arrowhead_bbox
arrowhead_bbox() -> Bbox
Return the bounding box of the single-headed arc arrowhead
Source code in src/momapy/core.py
1099 1100 1101 1102 1103 | |
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 | |
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 | |
arrowhead_length
arrowhead_length() -> float
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
1071 1072 1073 1074 1075 1076 1077 1078 | |
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
1080 1081 1082 1083 1084 1085 1086 1087 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
UnknownModulator
dataclass
UnknownModulator(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
referred_species: Species | BooleanLogicGate
)
Bases: _Modifier
Class for unknown modulators
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'5207e165-e336-46cd-80b8-70ab4c1260c4'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
referred_species
|
Species | BooleanLogicGate
|
The species the modifier refers to |
required |
UnknownNegativeInfluence
dataclass
UnknownNegativeInfluence(
*,
id_: str = get_uuid4_as_str(),
source: Species | BooleanLogicGate,
target: Species | None
)
Bases: UnknownModulation
Class for unknown negative influences
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'df0c4607-2569-464e-90a8-4b871639a195'
|
source
|
Species | BooleanLogicGate
|
The source of the influence |
required |
target
|
Species | None
|
The target of the influence |
required |
UnknownPhysicalStimulation
dataclass
UnknownPhysicalStimulation(
*,
id_: str = get_uuid4_as_str(),
source: Species | BooleanLogicGate,
target: Species | None
)
Bases: UnknownModulation
Class for unknown physical stimulations
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'800ef892-e34b-426d-b048-6431f8843ae0'
|
source
|
Species | BooleanLogicGate
|
The source of the influence |
required |
target
|
Species | None
|
The target of the influence |
required |
UnknownPhysicalStimulationLayout
dataclass
UnknownPhysicalStimulationLayout(
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 0.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (12, 4),
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 0.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_fill: NoneValueType | Color | None = white,
arrowhead_filter: NoneValueType | Filter | None = None,
arrowhead_stroke: NoneValueType | Color | None = black,
arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
arrowhead_stroke_dashoffset: float | None = None,
arrowhead_stroke_width: float | None = 1.0,
arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_height: float = 10.0,
arrowhead_width: float = 10.0
)
Bases: CellDesignerSingleHeadedArc
Class for unknown physical stimulation layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'183b32c0-7570-4944-909c-4daa3ee99107'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
The length the end of the arc will be shorten by |
0.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(12, 4)
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
The length the start of the arc will be shorten by |
0.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
arrowhead_filter
|
NoneValueType | Filter | None
|
The arrowhead filter of the arc |
None
|
arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The arrowhead stroke dasharray of the arc |
None
|
arrowhead_stroke_dashoffset
|
float | None
|
The arrowhead stroke dashoffset of the arc |
None
|
arrowhead_stroke_width
|
float | None
|
|
1.0
|
arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
The arrowhead transform of the arc |
None
|
arrowhead_height
|
float
|
|
10.0
|
arrowhead_width
|
float
|
|
10.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
1089 1090 1091 1092 1093 1094 1095 1096 1097 | |
arrowhead_bbox
arrowhead_bbox() -> Bbox
Return the bounding box of the single-headed arc arrowhead
Source code in src/momapy/core.py
1099 1100 1101 1102 1103 | |
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 | |
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 | |
arrowhead_length
arrowhead_length() -> float
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
1071 1072 1073 1074 1075 1076 1077 1078 | |
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
1080 1081 1082 1083 1084 1085 1086 1087 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
UnknownPositiveInfluence
dataclass
UnknownPositiveInfluence(
*,
id_: str = get_uuid4_as_str(),
source: Species | BooleanLogicGate,
target: Species | None
)
Bases: UnknownModulation
Class for unknown positive influences
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'9da4d562-49f9-4608-affa-78478482d435'
|
source
|
Species | BooleanLogicGate
|
The source of the influence |
required |
target
|
Species | None
|
The target of the influence |
required |
UnknownPositiveInfluenceLayout
dataclass
UnknownPositiveInfluenceLayout(
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 0.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (12, 4),
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 0.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_fill: (
NoneValueType | Color | None
) = NoneValue,
arrowhead_filter: NoneValueType | Filter | None = None,
arrowhead_stroke: NoneValueType | Color | None = black,
arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
arrowhead_stroke_dashoffset: float | None = None,
arrowhead_stroke_width: float | None = 2.0,
arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_height: float = 10.0,
arrowhead_width: float = 10.0
)
Bases: CellDesignerSingleHeadedArc
Class for unknown positive influence layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'0a9463cc-e8e4-494a-aa2a-23cade1c5957'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
The length the end of the arc will be shorten by |
0.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(12, 4)
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
The length the start of the arc will be shorten by |
0.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
arrowhead_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
arrowhead_filter
|
NoneValueType | Filter | None
|
The arrowhead filter of the arc |
None
|
arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The arrowhead stroke dasharray of the arc |
None
|
arrowhead_stroke_dashoffset
|
float | None
|
The arrowhead stroke dashoffset of the arc |
None
|
arrowhead_stroke_width
|
float | None
|
|
2.0
|
arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
The arrowhead transform of the arc |
None
|
arrowhead_height
|
float
|
|
10.0
|
arrowhead_width
|
float
|
|
10.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
1089 1090 1091 1092 1093 1094 1095 1096 1097 | |
arrowhead_bbox
arrowhead_bbox() -> Bbox
Return the bounding box of the single-headed arc arrowhead
Source code in src/momapy/core.py
1099 1100 1101 1102 1103 | |
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 | |
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 | |
arrowhead_length
arrowhead_length() -> float
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
1071 1072 1073 1074 1075 1076 1077 1078 | |
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
1080 1081 1082 1083 1084 1085 1086 1087 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 | |
points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 | |
self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |
UnknownTransition
dataclass
UnknownTransition(
*,
id_: str = get_uuid4_as_str(),
name: str | None = None,
sbo_term: SBOTerm | None = None,
metaid: str | None = None,
reversible: bool,
compartment: Compartment | None = None,
reactants: frozenset[Reactant] = frozenset(),
products: frozenset[Product] = frozenset(),
modifiers: frozenset[
Modulator | UnknownModulator
] = frozenset()
)
Bases: Reaction
Class for unknown transitions
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'13bf6342-1429-4ff6-b661-d7de61ef3544'
|
name
|
str | None
|
|
None
|
sbo_term
|
SBOTerm | None
|
|
None
|
metaid
|
str | None
|
|
None
|
reversible
|
bool
|
|
required |
compartment
|
Compartment | None
|
|
None
|
UnknownTransitionLayout
dataclass
UnknownTransitionLayout(
*,
_left_connector_fraction: float = 0.4,
_right_connector_fraction: float = 0.6,
reaction_node_height: float = 10.0,
reaction_node_width: float = 10.0,
reaction_node_segment: int = 1,
reaction_node_stroke: (
NoneValueType | Color | None
) = black,
reaction_node_stroke_width: float | None = 1.0,
reaction_node_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
reaction_node_stroke_dashoffset: float | None = None,
reaction_node_fill: (
NoneValueType | Color | None
) = white,
reaction_node_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
reaction_node_filter: (
NoneValueType | Filter | None
) = None,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 2.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 2.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_arrowhead_fill: (
NoneValueType | Color | None
) = black,
end_arrowhead_filter: (
NoneValueType | Filter | None
) = None,
end_arrowhead_stroke: (
NoneValueType | Color | None
) = black,
end_arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
end_arrowhead_stroke_dashoffset: float | None = None,
end_arrowhead_stroke_width: float | None = 1.0,
end_arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
start_arrowhead_fill: (
NoneValueType | Color | None
) = black,
start_arrowhead_filter: (
NoneValueType | Filter | None
) = None,
start_arrowhead_stroke: (
NoneValueType | Color | None
) = black,
start_arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
start_arrowhead_stroke_dashoffset: float | None = None,
start_arrowhead_stroke_width: float | None = 1.0,
start_arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
reversible: bool = False,
end_arrowhead_height: float = 8.0,
end_arrowhead_width: float = 15.0,
start_arrowhead_height: float = 8.0,
start_arrowhead_width: float = 15.0
)
Bases: _ReactionLayout, _ReactionNodeMixin
Class for unknown transition layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
_left_connector_fraction
|
float
|
|
0.4
|
_right_connector_fraction
|
float
|
|
0.6
|
reaction_node_height
|
float
|
|
10.0
|
reaction_node_width
|
float
|
|
10.0
|
reaction_node_segment
|
int
|
|
1
|
reaction_node_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
reaction_node_stroke_width
|
float | None
|
|
1.0
|
reaction_node_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
reaction_node_stroke_dashoffset
|
float | None
|
|
None
|
reaction_node_fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
reaction_node_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
reaction_node_filter
|
NoneValueType | Filter | None
|
|
None
|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'958543b0-e17b-4351-89ee-bcb3c57f1edb'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
|
2.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The path stroke dasharray of the arc |
None
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
|
2.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
end_arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
end_arrowhead_filter
|
NoneValueType | Filter | None
|
|
None
|
end_arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
end_arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
end_arrowhead_stroke_dashoffset
|
float | None
|
|
None
|
end_arrowhead_stroke_width
|
float | None
|
|
1.0
|
end_arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
start_arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
start_arrowhead_filter
|
NoneValueType | Filter | None
|
|
None
|
start_arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
start_arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
None
|
start_arrowhead_stroke_dashoffset
|
float | None
|
|
None
|
start_arrowhead_stroke_width
|
float | None
|
|
1.0
|
start_arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
|
None
|
reversible
|
bool
|
|
False
|
end_arrowhead_height
|
float
|
|
8.0
|
end_arrowhead_width
|
float
|
|
15.0
|
start_arrowhead_height
|
float
|
|
8.0
|
start_arrowhead_width
|
float
|
|
15.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_arrowhead_base |
Return the base anchor point of the double-headed arc end arrowhead |
end_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
end_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. |
end_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc end arrowhead |
end_arrowhead_length |
Return the length of the double-headed arc end arrowhead |
end_arrowhead_tip |
Return the tip anchor point of the double-headed arc end arrowhead |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the double-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_arrowhead_base |
Return the base anchor point of the double-headed arc start arrowhead |
start_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
start_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. |
start_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc start arrowhead |
start_arrowhead_length |
Return the length of the double-headed arc start arrowhead |
start_arrowhead_tip |
Return the tip anchor point of the double-headed arc start arrowhead |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
93 94 95 96 97 98 99 | |
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | |
end_arrowhead_base
end_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 | |
end_arrowhead_bbox
end_arrowhead_bbox()
Return the bounding box of the double-headed arc start arrowhead
Source code in src/momapy/core.py
1400 1401 1402 1403 1404 | |
end_arrowhead_border
end_arrowhead_border(point)
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 | |
end_arrowhead_drawing_elements
end_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 | |
end_arrowhead_length
end_arrowhead_length() -> float
Return the length of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1370 1371 1372 1373 1374 1375 1376 1377 | |
end_arrowhead_tip
end_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
1379 1380 1381 1382 1383 1384 1385 1386 | |
end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
982 983 984 985 986 987 988 989 990 991 | |
length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the double-headed arc path
Source code in src/momapy/core.py
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points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
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self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
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self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
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self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
Source code in src/momapy/celldesigner/core.py
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self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
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start_arrowhead_base
start_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
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start_arrowhead_bbox
start_arrowhead_bbox() -> Bbox
Return the bounding box of the double-headed arc start arrowhead
Source code in src/momapy/core.py
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start_arrowhead_border
start_arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
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start_arrowhead_drawing_elements
start_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc start arrowhead
Source code in src/momapy/core.py
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start_arrowhead_length
start_arrowhead_length() -> float
Return the length of the double-headed arc start arrowhead
Source code in src/momapy/core.py
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start_arrowhead_tip
start_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
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start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
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to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
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UnknownTriggering
dataclass
UnknownTriggering(
*,
id_: str = get_uuid4_as_str(),
source: Species | BooleanLogicGate,
target: Species | None
)
Bases: UnknownModulation
Class for unknown triggerings
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'8bb8433b-b450-4b03-a50d-c1a1534934e3'
|
source
|
Species | BooleanLogicGate
|
The source of the influence |
required |
target
|
Species | None
|
The target of the influence |
required |
UnknownTriggeringLayout
dataclass
UnknownTriggeringLayout(
*,
id_: str = get_uuid4_as_str(),
layout_elements: tuple[LayoutElement] = tuple(),
group_fill: NoneValueType | Color | None = None,
group_fill_rule: FillRule | None = None,
group_filter: NoneValueType | Filter | None = None,
group_font_family: str | None = None,
group_font_size: float | None = None,
group_font_style: FontStyle | None = None,
group_font_weight: FontWeight | float | None = None,
group_stroke: NoneValueType | Color | None = None,
group_stroke_dasharray: tuple[float] | None = None,
group_stroke_dashoffset: float | None = None,
group_stroke_width: float | None = None,
group_text_anchor: TextAnchor | None = None,
group_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
end_shorten: float = 0.0,
fill: NoneValueType | Color | None = None,
filter: NoneValueType | Filter | None = None,
path_fill: NoneValueType | Color | None = NoneValue,
path_filter: NoneValueType | Filter | None = None,
path_stroke: NoneValueType | Color | None = black,
path_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = (12, 4),
path_stroke_dashoffset: float | None = None,
path_stroke_width: float | None = 1.0,
path_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
stroke: NoneValueType | Color | None = None,
stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
stroke_dashoffset: float | None = None,
stroke_width: float | None = None,
segments: tuple[
Segment | BezierCurve | EllipticalArc
] = tuple(),
source: LayoutElement | None = None,
start_shorten: float = 0.0,
target: LayoutElement | None = None,
transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_fill: NoneValueType | Color | None = white,
arrowhead_filter: NoneValueType | Filter | None = None,
arrowhead_stroke: NoneValueType | Color | None = black,
arrowhead_stroke_dasharray: (
NoneValueType | tuple[float] | None
) = None,
arrowhead_stroke_dashoffset: float | None = None,
arrowhead_stroke_width: float | None = 1.0,
arrowhead_transform: (
NoneValueType | tuple[Transformation] | None
) = None,
arrowhead_bar_height: float = 8.0,
arrowhead_sep: float = 5.0,
arrowhead_triangle_height: float = 10.0,
arrowhead_triangle_width: float = 15.0
)
Bases: CellDesignerSingleHeadedArc
Class for unknown triggering layouts
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id_
|
str
|
The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element |
'cb8ffc01-c88c-4c38-8b74-c58cb67b9fe3'
|
layout_elements
|
tuple[LayoutElement]
|
The sub-layout elements of the group layout. These are part of the children of the group layout |
<dynamic>
|
group_fill
|
NoneValueType | Color | None
|
The fill color of the group layout |
None
|
group_fill_rule
|
FillRule | None
|
The fill rule of the group layout |
None
|
group_filter
|
NoneValueType | Filter | None
|
The filter of the group layout |
None
|
group_font_family
|
str | None
|
The font family of the group layout |
None
|
group_font_size
|
float | None
|
The font size of the group layout |
None
|
group_font_style
|
FontStyle | None
|
The font style of the group layout |
None
|
group_font_weight
|
FontWeight | float | None
|
The font weight of the group layout |
None
|
group_stroke
|
NoneValueType | Color | None
|
The stroke color of the group layout |
None
|
group_stroke_dasharray
|
tuple[float] | None
|
The stroke dasharray of the group layout |
None
|
group_stroke_dashoffset
|
float | None
|
The stroke dashoffset of the group layout |
None
|
group_stroke_width
|
float | None
|
The stroke width of the group layout |
None
|
group_text_anchor
|
TextAnchor | None
|
The text anchor of the group layout |
None
|
group_transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the group layout |
None
|
end_shorten
|
float
|
The length the end of the arc will be shorten by |
0.0
|
fill
|
NoneValueType | Color | None
|
The fill color of the arc |
None
|
filter
|
NoneValueType | Filter | None
|
The fill filter of the arc |
None
|
path_fill
|
NoneValueType | Color | None
|
|
<momapy.drawing.NoneValueType object at 0x7f3954141040>
|
path_filter
|
NoneValueType | Filter | None
|
The path filter of the arc |
None
|
path_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
path_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
|
(12, 4)
|
path_stroke_dashoffset
|
float | None
|
The path stroke dashoffset of the arc |
None
|
path_stroke_width
|
float | None
|
|
1.0
|
path_transform
|
NoneValueType | tuple[Transformation] | None
|
The path transform of the arc |
None
|
stroke
|
NoneValueType | Color | None
|
The stroke color of the arc |
None
|
stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The stroke dasharray of the arc |
None
|
stroke_dashoffset
|
float | None
|
The stroke dashoffset of the arc |
None
|
stroke_width
|
float | None
|
The stroke width of the arc |
None
|
segments
|
tuple[Union[Segment, BezierCurve, EllipticalArc]]
|
The path segments of the arc |
<dynamic>
|
source
|
LayoutElement | None
|
The source of the arc |
None
|
start_shorten
|
float
|
The length the start of the arc will be shorten by |
0.0
|
target
|
LayoutElement | None
|
The target of the arc |
None
|
transform
|
NoneValueType | tuple[Transformation] | None
|
The transform of the arc |
None
|
arrowhead_fill
|
NoneValueType | Color | None
|
|
Color(red=255, green=255, blue=255, alpha=1.0)
|
arrowhead_filter
|
NoneValueType | Filter | None
|
The arrowhead filter of the arc |
None
|
arrowhead_stroke
|
NoneValueType | Color | None
|
|
Color(red=0, green=0, blue=0, alpha=1.0)
|
arrowhead_stroke_dasharray
|
NoneValueType | tuple[float] | None
|
The arrowhead stroke dasharray of the arc |
None
|
arrowhead_stroke_dashoffset
|
float | None
|
The arrowhead stroke dashoffset of the arc |
None
|
arrowhead_stroke_width
|
float | None
|
|
1.0
|
arrowhead_transform
|
NoneValueType | tuple[Transformation] | None
|
The arrowhead transform of the arc |
None
|
arrowhead_bar_height
|
float
|
|
8.0
|
arrowhead_sep
|
float
|
|
5.0
|
arrowhead_triangle_height
|
float
|
|
10.0
|
arrowhead_triangle_width
|
float
|
|
15.0
|
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name) -> Point
Return an anchor point of the layout element
Source code in src/momapy/core.py
135 136 137 | |
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
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arrowhead_bbox
arrowhead_bbox() -> Bbox
Return the bounding box of the single-headed arc arrowhead
Source code in src/momapy/core.py
1099 1100 1101 1102 1103 | |
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
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arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
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arrowhead_length
arrowhead_length() -> float
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
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arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
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bbox
bbox() -> Bbox
Compute and return the bounding box of the layout element
Source code in src/momapy/core.py
73 74 75 76 | |
childless
childless() -> Self
Return a copy of the arc with no children
Source code in src/momapy/core.py
978 979 980 | |
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
573 574 575 576 577 | |
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
Source code in src/momapy/core.py
120 121 122 | |
descendants
descendants() -> list[LayoutElement]
Return the descendants of the layout element
Source code in src/momapy/core.py
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drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
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end_point
end_point() -> Point
Return the ending point of the arc
Source code in src/momapy/core.py
974 975 976 | |
equals
equals(other, flattened=False, unordered=False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
108 109 110 111 112 113 114 115 116 117 118 | |
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
101 102 103 104 105 106 | |
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
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length
length()
Return the total length of the arc path
Source code in src/momapy/core.py
966 967 968 | |
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
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points
points() -> list[Point]
Return the points of the arc path
Source code in src/momapy/core.py
958 959 960 961 962 963 964 | |
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
Source code in src/momapy/core.py
530 531 532 533 | |
self_children
self_children() -> list[LayoutElement]
Return the self children of the arc
Source code in src/momapy/core.py
954 955 956 | |
self_drawing_elements
self_drawing_elements()
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
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self_to_shapely
self_to_shapely() -> GeometryCollection
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
Source code in src/momapy/core.py
524 525 526 527 528 | |
start_point
start_point() -> Point
Return the starting point of the arc
Source code in src/momapy/core.py
970 971 972 | |
to_shapely
to_shapely(to_polygons: bool = False) -> GeometryCollection
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
124 125 126 127 128 129 130 131 132 133 | |